My list isn't necessarily all favorites.
PCThe Doom series (Including Doom 64(Unofficial PC Port))
The Quake series (Including Enemy Territory: Quake Wars)
The Half-Life(2) series (Including Opposing Force, Blue Shift, Portal, Episodes 1 and 2)
The Serious Sam series
Touhou 1-11 (
http://en.wikipedia.org/wiki/Touhou_Project )
NESSuper Mario Brothers 1-3
Legend of Zelda
Bubble Bobble
Mega Man 1-6
Bomberman
SNESLegend of Zelda: A Link To The Past
Super Mario All-Stars
Super Mario World
Chrono Trigger
Secret of Mana/Seiken Densetsu 2
Seiken Densetsu 3
Super Metroid
Final Fantasies 4, 5, and 6
Super Mario Kart
Donkey Kong Countries 1, 2, and 3
Super Mario RPG
(Super Mario World 2)Yoshi's Island
Mega Man X1-3
Sega GenesisSonic the hedgehog 1
Sonic the hedgehog 2
Sonic the hedgehog 3 and Knuckles
Sonic Spinball
Sega CDSonic CD (preferably the Japanese/Europe soundtrack)
N64Super Mario 64
Super Mario Kart
Legend of Zelda: Ocorina of Time
Banjo-Kazooie
Banjo-Tooie
Paper Mario
Goldeneye
Mario Party 1-3
Super Smash Brothers
Gameboy AdvanceMetroid Zero Mission
Metroid Fusion
Mario Kart Super Circuit
Super Mario Advance 1-4
Legend of Zelda: Four Swords (+ ALTTP remake)
Mario & Luigi Superstar Saga
WarioWare: Mega Microgame$!
WarioWare: Twisted!
Sega DreamcastSonic Adventure
Sonic Adventure 2
ChuChu Rocket
GamecubeLegend of Zelda: Wind Waker
Mario Kart Double Dash!!
Legend of Zelda: Ocorina of Time Master Quest
Legend of Zelda: Four Swords Adventures
Super Mario Sunshine
Paper Mario 2: The Thousand-Year Door
Sonic Adventure DX
Animal Crossing
Super Smash Brothers: Melee
Nintendo DSLegend of Zelda: Phantom Hourglass
New Super Mario Brothers
Mario & Luigi: Partners in Time
Mario Kart DS
WarioWare: Touched!
Super Mario 64 DS
Mario Party DS
Nintendo WiiLegend of Zelda: Twilight Princess
Super Mario Galaxy
Super Paper Mario
Super Smash Brothers: Brawl
Elebits
Geometry Wars: Galaxies
PlaystationCrash Bandicoot 1-3
Mega Man X4-6
Final Fantasy IX
I'll add more as I remember them.