OK, final lists, and description drafts for seasons 1 and 2 (others coming later)! In the case of ties in votes, I was the tie-breaker, so all of my suggestions went through. Note that I modified multiple season 1 descriptions. Since I mentioned when people started liking Rarity, I realized I should do the same for the CMC, since people hated them for much of season 1. Oddly enough, I recall that the episode that swayed opinion was "The Cutie Mark Chronicles", but the reason was that it was a CMC episode that was actually more about the main characters. It's a bit odd of an explanation, and it's unrelated to why people consistently started liking them later, so I instead went for adding a vague explanation to "Call of the Cutie".
EDIT: Using this post to host the latest updated versions.
Season 1
1. "Friendship Is Magic - Part 1"
2. "Friendship Is Magic - Part 2"
Twilight Sparkle learns of the return of the evil Nightmare Moon, but her mentor, Princess Celestia, tells her to make friends in Ponyville instead of worrying. This story has some "early installment weirdness" and does not reflect the rest of the series in some respects, but is still important to watch.
3. "The Ticket Master" - Twilight Sparkle, Mane Six
* This starts a plotline continued by episodes 14 and 26.
4. "Applebuck Season" - Applejack, Mane Six
5. "Griffon the Brush Off" - Pinkie Pie, Rainbow Dash
Rainbow Dash's visiting friend, Gilda the griffon, starts bullying Pinkie Pie and others behind Rainbow's back. Gilda's unique nature made her a popular (though not well-liked) character in the early fandom.
6. "Boast Busters" - Twilight Sparkle
The Great and Powerful Trixie comes to town boasting of her magic skills, but Twilight is unwilling to demonstrate her own. Trixie is one of the most popular one-off characters to come out of season 1.
7. "Dragonshy" - Fluttershy, Mane Six
A dragon is causing problems, so the heroes go to confront it, despite Fluttershy's fear. Often considered one of the best "first episodes" to show someone.
8. "Look Before You Sleep" - Applejack, Rarity, Twilight Sparkle
9. "Bridle Gossip"
Twilight is critical of the town's irrational fear of a zebra that lives in the Everfree Forest, until she and her friends all wake up with what appear to be curses. Introduces Zecora and includes the most popular comedy scene of the early fandom.
10. "Swarm of the Century" - Mane Six
11. "Winter Wrap Up" - Twilight Sparkle, Mane Six
Twilight is excited to join in on the festival to end winter, but has a hard time finding a place. This is the first episode to include a full-fledged musical number, and it took the fandom by storm.
12. "Call of the Cutie"
Apple Bloom, Applejack's sister, realizes that she is one of the few ponies in her class who doesn't have a cutie mark (a symbol on her flank), so she joins two other fillies, Sweetie Belle and Scootaloo, to form the Cutie Mark Crusaders. Unpopular at first, they grew on fans by the end of the season.
13. "Fall Weather Friends" - Applejack, Rainbow Dash
14. "Suited for Success" - Rarity, Mane Six
Rarity offers to make dresses for her friends, but they quickly start making unreasonable demands. Before this point, Rarity had few fans, but this episode marks a shift in focus that made her more popular, showcasing her artistic side.
15. "Feeling Pinkie Keen" - Twilight Sparkle, Pinkie Pie
* Introduces Pinkie's ability to predict the near future, Pinkie Sense. The moral of this episode alarmed many people when it aired, due to being perceived as anti-science and pro-religion, but the show crew has clarified that it was not their intention.
16. "Sonic Rainboom" - Rainbow Dash, Rarity, Mane Six
Rainbow Dash enters an athletic competition judged by her idols, the Wonderbolts, but gets overwhelmed by the pressure. This is another popular "first episode".
17. "Stare Master" - Fluttershy, Cutie Mark Crusaders
* Introduces Fluttershy's hypnotic Stare.
18. "The Show Stoppers" - Cutie Mark Crusaders
19. "A Dog and Pony Show" - Rarity, Spike, Mane Six
20. "Green Isn't Your Color" - Fluttershy, Rarity, Twilight Sparkle, Pinkie Pie
Rarity tries to impress a famous fashion photographer, Photo Finish, but becomes jealous when Fluttershy catches her eye instead.
21. "Over a Barrel" - Mane Six
22. "A Bird in the Hoof" - Fluttershy, Twilight Sparkle
23. "The Cutie Mark Chronicles"
The Cutie Mark Crusaders learn about how the Mane Six all gained their cutie marks. Rainbow Dash's story in particular becomes important much later.
24. "Owl's Well That Ends Well" - Spike, Twilight Sparkle
* Introduces Twilight's pet owl, Owlowicious.
25. "Party of One" - Pinkie Pie, Mane Six
When Pinkie believes that her friends are intentionally avoiding her, she goes a bit crazy.
26. "The Best Night Ever" - Mane Six
The girls are all excited about attending the Grand Galloping Gala, but the night doesn't go as expected. This episode references "The Ticket Master" and "Suited for Success", but they are not necessary to follow the story. Introduces Spitfire and Soarin' of the Wonderbolts.
Season 2
1. "The Return of Harmony - Part 1"
2. "The Return of Harmony - Part 2"
The heroes must face an ancient spirit of chaos, Discord, played by John de Lancie (Q from Star Trek: The Next Generation), who aims to sever their connections with the Elements of Harmony.
3. "Lesson Zero" - Twilight Sparkle, Mane Six
In this very meta story, Twilight realizes that she hasn't learned a friendship lesson in almost a week, and goes a bit crazy looking for one before time runs out. This story modifies how the end-of-episode moral is handled.
4. "Luna Eclipsed"
Princess Luna visits Ponyville on a Halloween-style holiday celebrating Nightmare Moon's original defeat. Properly introduces Luna, in her "fully powered" form. It still takes another season for Luna to do anything after this, by the way.
5. "Sisterhooves Social" - Sweetie Belle, Rarity, Applejack
Sweetie Belle wants to attend the Sisterhooves Social with her sister, Rarity, but after a fight between them, Sweetie decides that Applejack makes for a better sister.
6. "The Cutie Pox" - Apple Bloom, Zecora
7. "May the Best Pet Win!" - Rainbow Dash, Fluttershy
* Introduces Rainbow Dash's pet tortoise, Tank.
8. "The Mysterious Mare Do Well" - Rainbow Dash, Mane Six
9. "Sweet and Elite" - Rarity
During a visit to Canterlot, Rarity becomes popular among the upper crust and puts off returning to Ponyville. Notably demonstrates that Rarity can carry an episode without the rest of the main cast.
10. "Secret of My Excess" - Spike, Twilight Sparkle, Rarity
After his birthday, Spike's desire for more presents causes his dragon instincts to go out of control.
11. "Family Appreciation Day" - Apple Bloom, Apple Family
* Reveals how Ponyville was founded.
12. "Baby Cakes" - Pinkie Pie
* Pinkie's landlords, the Cakes, have twins.
13. "Hearth's Warming Eve" - Mane Six
* Reveals how Equestria was founded.
14. "The Last Roundup" - Applejack, Mane Six
* Gives background character Derpy her first prominent appearance--and last one for a while.
15. "The Super Speedy Cider Squeezy 6000" - Apple Family
When the Apple Family starts selling their hoof-made apple cider, brothers Flim and Flam arrive with a cider-making machine, leading to a Music Man style song and a contest of horse vs. machine.
16. "Read It and Weep" - Rainbow Dash
Rainbow Dash becomes addicted to a Daring Do book while she is stuck in the hospital, and doesn't want anyone to know. Contains a story within the story inspired by Indiana Jones.
17. "Hearts and Hooves Day" - Cutie Mark Crusaders
After learning that their teacher, Cheerilee, doesn't have a boyfriend, the Cutie Mark Crusaders take it upon themselves to find the perfect stallion, even if it takes a love potion.
18. "A Friend in Deed" - Pinkie Pie
Following one of the catchiest songs of the show, Pinkie Pie meets Cranky Doodle Donkey and is shocked that he doesn't want to be her friend. Note that some people dislike how Pinkie acts in this episode.
19. "Putting Your Hoof Down" - Fluttershy
20. "It's About Time" - Twilight Sparkle, Pinkie Pie, Spike
Twilight is visited by her future self, who disappears before she can complete her warning. Thus, Twilight goes a bit crazy. The main story is stand-alone, but some details introduced are relevant to the season 4 and 5 finales.
21. "Dragon Quest" - Spike, Twilight Sparkle
22. "Hurricane Fluttershy" - Fluttershy, Rainbow Dash
All of the Ponyville pegasi have to work together for a task, but Fluttershy feels she'll just hold them back. Features an 80's training montage, and demonstrates a softening of Rainbow Dash's character.
23. "Ponyville Confidential" - Cutie Mark Crusaders
24. "MMMystery on the Friendship Express" - Pinkie Pie, Twilight Sparkle
25. "A Canterlot Wedding - Part 1"
26. "A Canterlot Wedding - Part 2"
Twilight's brother (just introduced), Shining Armor, is getting married to Princess Cadance (just introduced), but Twilight finds the situation suspicious. The early fandom was dreading this episode, but it turned out to be a sensation. Contains the first Disney-style villain song of the series.
Season 3
1. "The Crystal Empire - Part 1"
2. "The Crystal Empire - Part 2"
When the Crystal Empire returns after 1000 years, Twilight is tasked with protecting it from King Sombra with her friends, but to move on to her next level of study, she's told to stop him herself.
3. "Too Many Pinkie Pies" - Pinkie Pie, Mane Six
4. "One Bad Apple" - Cutie Mark Crusaders
* Introduces Apple Bloom's cousin, Babs Seed.
5. "Magic Duel" - Twilight Sparkle, Zecora
Trixie (season 1's "Boast Busters") returns with a magical amulet, challenging Twilight to a Sword in the Stone style magic duel.
6. "Sleepless in Ponyville" - Scootaloo, Rainbow Dash, Luna
Scootaloo is scared by Rainbow Dash's ghost story during a camping trip, but hides her fear to impress her, only to start getting nightmares. This episode marks a major shift in the relationship of those two characters, and gives Luna something to do.
7. "Wonderbolts Academy" - Rainbow Dash, Wonderbolts
8. "Just for Sidekicks" - Spike
* This episode occurs simultaneously with "Games Ponies Play".
9. "Apple Family Reunion" - Applejack, Apple Family
10. "Spike at Your Service" - Spike, Applejack
11. "Keep Calm and Flutter On
Fluttershy is tasked with reforming Discord--something that not even her friends believe she can do. The ending is rushed, but it is revisited in season 4.
12. "Games Ponies Play" - Mane Six, Cadance
* This episode occurs simultaneously with "Just for Sidekicks", and starts a plotline continued by season 4 episodes 5, 10, and 24.
13. "Magical Mystery Cure"
Twilight discovers that her friends' cutie marks--and destinies--have been switched. This full-musical episode rushes through plot developments clearly intended for a series finale (which it was for a time), but contains some of the best songs of the series. The ending is explored more in season 4.
Movie - Equestria Girls
After the events of "Magical Mystery Cure", Twilight's Element of Magic is stolen. She follows the thief through a portal leading to another dimension, where she turns into a human and all of her friends are humans attending high school. Many dislike the premise of a high school alternate universe, but many also find these movies enjoyable. The Equestria Girls movies reference the events of the series, but the series doesn't acknowledge the movies, so they are completely optional.
Season 4
1. "Princess Twilight Sparkle - Part 1"
2. "Princess Twilight Sparkle - Part 2"
When the Everfree Forest goes out of control, the Mane Six once again journey into it, but things aren't the same now that Twilight is a princess, as Discord enjoys rubbing in. Even if you're just watching these boxed episodes, make sure to watch at least one of episodes 8, 10, 11, 16, and 21 of this season before watching the season finale.
3. "Castle Mane-ia" - Mane Six
The girls all separately find themselves at the ruins of the Castle of the Two Sisters, unknowingly scaring each other. This story modifies how the end-of-episode moral is handled.
4. "Daring Don't" - Rainbow Dash, Mane Six
* Reveals that Daring Do (season 2's "Read It and Weep") is real.
5. "Flight to the Finish" - Scootaloo, Cutie Mark Crusaders, Rainbow Dash
Scootaloo becomes ashamed of the fact that she can't fly at her age. This episode continues a plotline started by season 3's "Games Ponies Play", and continued by "Rainbow Falls" and Equestria Games", but they aren't necessary to follow this story.
6. "Power Ponies" - Spike, Mane Six
7. "Bats!" - Fluttershy, Applejack, Mane Six
* Fluttershy turns into a vampire for a bit here, which sometimes comes up later.
8. "Rarity Takes Manehattan" - Rarity, Mane Six
Rarity helps one of her rivals in a fashion competition, only for her to turn around and plagiarize her designs, making Rarity question her generosity. To everyone's surprise, minor character Coco Pommel was popular with fans.
9. "Pinkie Apple Pie" - Pinkie Pie, Applejack, Apple Family
Pinkie discovers ambivalent evidence that she's distantly related to the Apple Family, and to find concrete proof, they go on a road trip to talk to the Apple Family's historian. Hijinks ensue.
10. "Rainbow Falls" - Rainbow Dash, Wonderbolts
* Gives a prominent role to background character Bulk Biceps, and marks the return of Derpy after a long absence.
11. "Pinkie Pride" - Pinkie Pie
In this full-musical episode, a new "super duper party pony" arrives: Cheese Sandwich, played by comedy singer Weird Al. When he sweeps the town off its feet, Pinkie questions if she's really meant to plan parties.
12. "Three's A Crowd" - Twilight Sparkle, Discord, Cadance
13. "Simple Ways" - Rarity, Applejack
14. "Filli Vanilli" - Fluttershy, Rarity
When a member of Rarity's a cappella group, the Pony Tones, loses his voice, Fluttershy steps up to replace him--provided that she can hide behind the curtain and dub over him while he lip-synches.
15. "Twilight Time" - Cutie Mark Crusaders, Twilight Sparkle
The Cutie Mark Crusaders realize that Twilight is a lot more popular now that she's a princess, and take advantage of their friendship to become cool with the other kids.
16. "It Ain't Easy Being Breezies" - Fluttershy, Mane Six
17. "Somepony to Watch Over Me" - Apple Bloom, Applejack
18. "Trade Ya!" - Mane Six
19. "Maud Pie" - Pinkie Pie, Mane Six
Pinkie is excited to introduce one of her sisters, Maud, to her friends, but they have a hard time getting along with her. Maud was an instant hit with the fans. She isn't one of the sisters seen in season 1's "The Cutie Mark Chronicles", but they do appear later.
20. "For Whom the Sweetie Belle Toils" - Sweetie Belle, Rarity, Luna
After a fight between them, Sweetie Belle sabotages a dress that Rarity made for an important client, and she starts having nightmares.
21. "Leap of Faith" - Applejack, Apple Family
22. "Testing Testing 1, 2, 3" - Rainbow Dash, Twilight Sparkle, Mane Six
Only one thing stands in the way of Rainbow Dash's goal of joining the Wonderbolts Reserves: the written exam. She is forced to turn to Twilight for help with studying.
23. "Inspiration Manifestation" - Spike, Rarity
24. "Equestria Games" - Spike
25. "Twilight's Kingdom - Part 1"
26. "Twilight's Kingdom - Part 2"
Twilight feels that she hasn't lived up to her title as princess. Meanwhile, Discord is sent to track down the evil Tirek, an update to the villain of the original 80's My Little Pony TV special. This will decide the fates of both Twilight and Discord, and solve the mystery of the locked chest. Features a great song sung by all four princesses.
Movie - Equestria Girls: Rainbow Rocks
After the events of "Twilight's Kingdom", three sirens from Equestria enter Canterlot High's Battle of the Bands, and while the "Humane Five" are able to bring in pony Twilight for help, it may be up to the reformed Sunset Shimmer to save the day. This movie is filled with songs, and many enjoyed seeing Sunset redeem herself. Again, these movies are completely optional.
Season 5
1. "The Cutie Map - Part 1"
2. "The Cutie Map - Part 2"
A mysterious map in Twilight's castle activates, leading the heroes to a strange town where everyone has the same cutie mark: an equal sign. This is the first two-parter to not focus on Twilight significantly more than the other main characters. The map sends the heroes on missions periodically throughout this season.
3. "Castle Sweet Castle" - Twilight Sparkle, Mane Six, Spike
4. "Bloom & Gloom" - Apple Bloom, Apple Family, Cutie Mark Crusaders, Luna
After Apple Bloom learns that her cousin, Babs (season 3's "One Bad Apple"), has gotten her cutie mark, she once again becomes anxious about getting her own. One day, she finally wakes up with a cutie mark, but it's one she doesn't want.
5. "Tanks for the Memories" - Rainbow Dash
* Five seasons in, this contains Rainbow Dash's first solo song of the show.
6. "Appleoosa's Most Wanted" - Cutie Mark Crusaders, Applejack
7. "Make New Friends but Keep Discord" - Discord, Fluttershy
The Grand Galloping Gala (season 1's "The Best Night Ever") has arrived again, and Discord is aghast when Fluttershy invites someone else as her plus-one. To show that he's not jealous, he invites the Smooze, an update to the villain of the 80's My Little Pony theatrical movie.
8. "The Lost Treasure of Griffonstone" - Rainbow Dash, Pinkie Pie
The map sends Rainbow and Pinkie to the griffon city of Griffonstone, where they encounter Gilda (season 1's "Griffon the Brush-Off").
9. "Slice of Life" - Background Characters
While the heroes fend off a monster, the town prepares for the wedding of Cranky and Matilda (season 2's "A Friend in Deed"). This is the 100th episode, and it chooses to celebrate the various background and side characters that have appeared throughout the show. Even if you haven't paid too much attention to them, the episode is still an enjoyable watch.
10. "Princess Spike" - Spike, Twilight Sparkle, Cadance
11. "Party Pooped" - Pinkie Pie, Twilight Sparkle, Mane Six
When a diplomatic meeting with Prince Rutherford, leader of the yaks, goes bad, everyone expects Pinkie to improve his mood, and she becomes overwhelmed by the pressure.
12. "Amending Fences" - Twilight Sparkle, Spike
Twilight decides to meet up with her old classmates from Magic School after realizing how bad a friend she used to be to them. After "Slice of Life", this was an unexpected second showcase of background characters, and many like it even more.
13. "Do Princesses Dream of Magic Sheep?" - Luna, Mane Six
14. "Canterlot Boutique" - Rarity
Rarity fulfills her dream of opening a shop in Canterlot (from the first episode), but finding success there may require giving up what she enjoys about dressmaking. The Canterlot shop becomes a recurring location.
15. "Scare Master" - Fluttershy, Mane Six
16. "Rarity Investigates!" - Rarity, Rainbow Dash, Wonderbolts
Rainbow Dash is finally flying with the Wonderbolts, but it proves short-lived when she is accused of a crime against them. It's up to Rarity to prove her innocence, as a film noir detective. The mystery is very simple, but Rarity's narration makes it great.
17. "Made in Manehattan" - Rarity, Applejack
* This episode occurs simultaneously with "Brotherhooves Social".
18. "Brotherhooves Social" - Apple Bloom, Apple Family
* This episode occurs simultaneously with "Made in Manehattan".
19. "Crusaders of the Lost Mark"
The Cutie Mark Crusaders help one of their classmates compete in a class president election against Diamond Tiara, who has tormented them since season 1's "Call of the Cutie", but end up discovering another side to her. This is a full-musical episode, and is a must-watch even if you aren't a fan of Cutie Mark Crusader episodes.
20. "The One Where Pinkie Pie Knows" - Pinkie Pie, Cadance, Twilight Sparkle
* Reveals that Cadance is pregnant.
21. "Hearthbreakers" - Pinkie Pie, Applejack, Apple Family
The Apples visit the Pies to celebrate Hearth's Warming (a Christmas-style holiday), but they are confused by their holiday traditions. Properly introduces the rest of Pinkie's family, and Pinkie's other sisters, Limestone and Marble, were instant hits with the fans. Note that even though they refer to each other as cousins, the Apples and Pies are distantly related at best.
22. "What About Discord?" - Twilight Sparkle, Discord, Mane Six
23. "The Hooffields and McColts" - Twilight Sparkle, Fluttershy
24. "The Mane Attraction" - Applejack
* Guest stars Tony award winner Lena Hall, who sings in this episode.
25. "The Cutie Re-Mark - Part 1"
26. "The Cutie Re-Mark - Part 2"
Starlight Glimmer, from the season premiere, attempts to demonstrate to Twilight that her friendships aren't important by using the power of the map to rewrite the past, so that the Mane Six never met. Showcases various alternate realities, each with a different villain winning.
Movie - Equestria Girls: Friendship Games
The Twilight Sparkle native to the human world finally appears, as a student from a rival school who is curious about the strange events at Canterlot High. When the schools meet for an athletic competition, Twilight learns about friendship from the Humane Five and Sunset, even as her principal promotes hatred and the device she built to scan for magic starts absorbing large amounts of it.