- Stamp Collecting* (Route A)
- Jackass' Request* (Route A)
- Robot Dojo questline* (Route A/B)
- 11B's Memento (Route A, quest is found in the Bunker)
- YoRHa Betrayers (Route A)
- Retrieve the Confidential Info* (Route A)
- Jean-Paul's Melancholy* (Route A)
- The Wandering Couple (Route A/B)
- Half-wit Inventor (Route A/B/C, you need lots of money)
- (Operator 6O) Terminal Repairs -> Find A Present (Route A)
- (Operator 21O) Data Analysis Freak -> Data Analysis Freak 2 (Route B)
- Lord of the Valley* (Route A)
- Machine Examination 1/2* (Route A)
- Treasure Hunt at the Castle (Route A/B/C)
- (Minor spoiler, but just in case)
's Memories (Route A/B) -->
's Determination
- Camp Development > Anemone's Past* (Route A)
- Heritage of the Past (Route B, gives you 9S' best weapon once upgraded to Lv4)
- Amnesia (Route B)
- Idiot Savant (Route B)
- The Recluse questline (Route B)
- (Minor spoiler, but again, just in case)
's Request (Route C)
- (Minor spoiler)
's Errand (Route C)
- The Twins' Request (Route C)
- Play With Us! (Route C)
- Gathering Keepsakes (Route C)
If you happen to come across these sidequests and recognize it being a part of this list, just know that I recommend doing them. Maybe they're funny, sad, creepy, nostalgic for Nier 1 players, foreshadow something, further flesh out a character/theme/world, has a dark twist, gives you a pod program, or maybe you don't have to move a muscle in order to complete it. Don't stress about finding all of them (unless that's the type of person you are I guess), but yea, enjoy. There are some in this list that I don't just recommend, but consider to be "essential", but honestly I don't want to point them out, lest I inadvertently spoil or ruin anything for you, by having you wonder why said quest is "essential" to begin with.
If I put a "*" next to a quest, it's because I'm not entirely sure whether or not said quest can be done in another route. If I used "->", it's because the previous quest is needed in order to access the subsequent one.
Some sidequests disappear once the main story directs you to the (minor spoilers)
City, so be aware of that. As you can see above however, if you fail to complete certain sidequests, they may be available in the next route. If you started a sidequest in say, Route A, and finish Route A without completing it, you will have to restart that specific quest all over again, assuming it is actually in Route B and onwards.
Regardless, no sidequests are permanently missable. And again, I'd advise you to stick to tackling sidequests after you've obtained the ability to fast travel.