I've got up to 101 in order, with the preferred platform/release/controller/settings if applicable
1. Marathon: Infinity (Aleph One OpenGL with high res texture packs but original HUD)
2. Marathon 2: Durandal (Classic Mac or Aleph One with original textures and low res software rendering)
3. Dark Souls (PS3 original un-updated US release disc)
4. Super Mario 64 (N64 on CRT)
5. Metroid (NES on CRT)
6. Minecraft (Win, latest version is great, but also the alpha version around when they first added minecart tracks had the most interesting land formations and caves)
7. Riven: the Sequel to Myst (Classic Mac on CRT)
8. Myth: the Fallen Lords (640x480 Glide driver)
9. Sea of Thieves (Xbox One Controller)
10. Zelda II: The Adventure of Link (NES on CRT)
11. Obduction (Win, not the VR version)
12. Final Fantasy IV (SFC, "hardtype" patched with translation if needed)
13. Risen (Win, mouse and keyboard)
14. Thief: the Dark Project (Win, 640x480 software on CRT, mouse and keyboard)
15. Doom 2016 (Win, Xbox One Controller, Multiplayer only)
16. Sagaia (Genesis, CRT, Seimistu LS-32 Stick)
17. Mario Kart 64 (N64 on CRT)
18. Quake III Arena (Win, 90hz+, mouse and keyboard)
19. Spelunky (Win with handle-less Wii Classic Controller)
20. The Witness (Win, mouse and keyboard)
21. Super Mario Sunshine (GC)
22. Final Fantasy (PS1, Original NES difficulty and magic system)
23. Gadget: Invention, Travel, Adventure (Mac)
24. Metroid Prime (GC)
25. Nintendo Land (Wii U)
26. Portal (Win, mouse and keyboard)
27. Descent II (Rebirth source port 640x480, unfiltered textures, with Xbox One controller, play your own music)
28. New Super Luigi U (Wii U)
29. Silent Hill (PS1)
30. Star Wars: Jedi Knight (Win, 640x480 Software Rendering)
31. Hexen II (Win, 320x200 Software Rendering, reduce gamma and brightness below minimum with your GPU settings)
32. Quest for Glory I (VGA DOS rerelease, Roland Sound Canvas MIDI)
33. Xenogears (PS1)
34. F-Zero GX (GC, CRT)
35. The Legend of Zelda: Majora's Mask (N64)
36. Ico (PS2, CRT)
37. Super Monkey Ball (GC, Monkey Target and Single Player)
38. Grand Theft Auto III (PS2 on CRT)
39. Super Mario Bros. 3. (NES, CRT)
40. Resident Evil 1 Remake (GC, tank controls, R to run)
41. Kid Icarus (NES, CRT)
42. Destiny 1.0 (PS4, avoid all content after the first two expansions)
43. Suikoden II (PS1)
44. Metroid II: Return of Samus (GB, black and white mode only)
45. Fez (Vita unless you have an OLED TV)
46. Legend of Grimrock (Win, mouse and keyboard)
47. Lode Runner XBLA (Xbox 360 has one frame less lag than Xbox One)
48. R-Type Delta (PS1, CRT, Seimitsu LS-32 Stick)
49. Star Fox (SNES)
50. NaissanceE (Win, mouse and keyboard)
51. Mr. Do! (Arcade if possible, 4-way restricted Arcade Stick)
52. Solomon's Key (Arcade if possible, 4-way restricted Arcade Stick)
53. Duke Nukem 3D (Win, 20th Anniversary World Tour for the new expansion, mouse and keyboard)
54. Battle Garegga (Saturn on CRT has least input lag, Seimitsu LS-32 Stick)
55. Blood (NBlood with mouse, reduce gamma and brightness below minimum with your GPU settings)
56. Fallout New Vegas (Win)
57. Grand Theft Auto: San Andreas (PS2 modded with hard drive)
58. Donkey Kong Country Returns (Wii on CRT with anamorphic widescreen)
59. Shadow of the Colossus (PS2 on CRT or PS4 remake both good in different ways)
60. Pikmin (GC)
61. Sine Mora EX (Xbox One Controller, Letterboxed, Hungarian Voice Over)
62. Fire Emblem: Path of Radiance (GC)
63. Grand Theft Auto V (Win)
64. Donkey Kong '94 (GB, black and white mode only)
65. Overload (Win, Xbox One Controller)
66. Half Life 1 (PS2 on CRT, mouse and keyboard)
67. Super Mario Bros (NES on CRT)
68. Wave Race 64 (N64 on CRT)
69. Animal Crossing (GC)
70. Dark Souls II (Win, original version not SotFS)
71. N++ (Win, handle-less Wii Classic Controller)
72. Braid (Win)
73. Trials HD (Win, Xbox One Controller)
74. MotorStorm (PS3)
75. F-Zero (SNES on CRT)
76. The Legend of Zelda: A Link to the Past (SNES on CRT)
77. Rez Infinite (PSVR)
78. Final Fantasy IX (PS1)
79. Noby Noby Boy (PS3)
80. Hotline Miami (Win, mouse and keyboard)
81. Marble it Up! (Win, mouse and keyboard)
82. Kororinpa Marble Mania (Wii, most sensitive ball has best control)
83. Unreal Tournament (Win, 400x300 Software Rendering on CRT)
84. Resident Evil 4 (GC on CRT)
85. Beetle Adventure Racing (N64 on CRT)
86. Zack and Wiki (Wii)
87. Hot Shots Golf: Open Tee 2 (PSP has one frame less input lag than Vita)
88. Rocket: Robot on Wheels (N64)
89. Frequency (PS2 on CRT)
90. Escape Goat 2 (Win, handle-less Wii Classic Controller)
91. Maximo: Ghosts to Glory (PS2 on CRT)
92. Banjo Kazooie (N64 on CRT)
93. Doom (Just Episode 1 and Episode 5: Sigil with Buckethead music, GZDoom, original lighting, no texture filtering, mouse and keyboard)
94. Quake (Win, 400x300 Software Rendering, also Arcane Dimensions at 1280x720 Hardware Rendering, mouse and keyboard, play your own music)
95. Castlevania (NES on CRT)
96. Nex Machina (PS4 for perfect frame pacing)
97. Galactic Attack (Saturn on CRT, Seimitsu LS-32)
98. Resident Evil 7 (PSVR, enable smooth turning, disable vignette effect)
99. Grip: Combat Racing (Win, Xbox One Controller)
100. Volgarr the Viking (Win, handle-less Wii Classic Controller)
101. Dariusburst: Chronicle Saviours (Win, all DLC, G-Sync 120hz+ with Rivatuner to force 60fps limit to minimize input lag, Seimitsu LS-32 Joystick)
unordered additions
Border Down, The Legend of Zelda: Ocarina of Time, Stephen's Sausage Roll, FTL, Journey, Uncharted: The Lost Legacy, Verlet Swing, Contra III, Eggerland, Baldur's Gate 1, Xanadu Next, Blazing Chrome, Arthur Quest for Excalibur, Crysis 2, Bloodbourne, The Hidden: Source, Deadly Rooms of Death, Silent Hill 2&3, Crystal Quest, Super Metroid, Final Fantasy 5&8, Soul Blazer, Castlevania 3/4/Rondo/SOTN, Octahedron, Galaga, Celeste, Sonic Mania, Hyperrogue, Life is Strange, Human Fall Flat, Under Defeat, Mike Tyson's Punch Out, Ultimate Chicken Horse, Dragon Warrior 2, Dragon Quest XI, Superhot, Tomba!, Mega Man 1, Warhammer Vermintide 1&2, Refunct, Grow Home, Rad Racer, Crash Commando, Rusty's Real Deal Baseball, Actrasier, The New Tetris, Mario Power Tennis, Mario Gold Toadstool Tour, Haunting Ground, Mario vs Donkey Kong, Vib Ribbon, Ecco Defender of the Future, Metal Black, Obsidian, Viriax, Gothic, Crashmo, The Stanley Parable, Inversus, Shadowgate, SimCity B&W, Return to Dark Castle, Millipede, Inside, Hexen, Battle-Girl, Mario vs Donkey Kong 2, Rocket League, Yoshi Touch and Go, Yoshi's Island, The Pinball Arcade, Return to Castle Wolfenstein, Drive Club, Thief 2014, Rygar the Legendary Adventure, Faxanadu, Rygar, Motorstorm Pacific Rift, Brandish the Dark Revenant, Kid Icarus Uprising, Dirt 2, Mirror's Edge, Spectraball, The Talos Principle, Totally Accurate Battle Simulator, Besiege, Dark Messiah of Might and Magic, Cut the Rope, Wave Race Blue Storm, Midnight Club 2, F-Zero X, Wipeout HD, Wild Guns, R-Type 1&2, Demon's Souls, Eldritch, Cities Skylines, Sports Champions, Pac Man Championship Edition, Zelda Twilight Princess, Zelda Link's Awakening, Half Life 2, Milon's Secret Castle, Super Mario Bros. 2, Virtua Fighter 4, Bionic Commando Rearmed, Heart of Darkness, Myst, Out of this World, Radiant Silvergun, Bombastic, Wario World, Mario Kart 7&8