NES: Duck Hunt
SNES: Super Mario World
Gamecube: Resident Evil 4. If we're talking exclusives only MGS the Twin Snakes.
Wii: SSBB
PS1: Final Fantasy VII - best game of all time.
PS2:God of War or FFXII, impossible to choose.
PS3: MGS4, I'm near 100 percent certain nothing will top it for me this gen.
Xbox 360: Gears of War hands down.

PC Mafia:A really great game which got sidelined by the arrival of GTA III

NES Contra : This was the first game which made me realise playing games took some skills.

SNES Chrono Trigger: One of my favorites, the game has the best production values for its time, highly re-playable,a true masterpiece

PSX Symphony Of The Night : probably the best Castlevania game yet,didnt re-play any other game on the PS nearly as much as this

N64 The most obvious choice ever Ocarina Of Time

GBA Advance Wars : Great fun, one of the best portable games for me

NES: Super Mario Bros---the game that revived games, come on!
SNES: Super Metroid ----One of the most balanced and perfectly paced games ever made, invented speed running as we know it
N64: Ocarina of Time ----continued Mario 64's success of inventing how games are played in 3D, nearly every single game after OoT has used ideas it created
Gamecube: Metroid Prime---invented the FPA genre, even today it's world is the most natural and detailed, it truly feels "living" and no game since has been able to replicate it (except maybe the other Metroid games)
PS1: Metal Gear Solid---Just a really good game for the console.
Xbox: Halo---I hate to say it as i hate this game in every possible way, but it did revive console FPS's and made them what they are today.

PC Civilization: Huge toss up between many games here but this one gets it in the end.

SNES: Super Mario RPG: I know this one will be controversial but it's my personal favourite of the many RPGs the SNES was famous for.

N64: LoZ: OoT: It was between this and SM64 and really I don't think any game has ever managed to beat the feeling of immersion and involvement that this game created.

PSX: GT2: Only game I ever really played on the PSX, perhaps not a masterpiece but the best the PS2 had to offer.

GB/GBC: Pokemon Red/Blue: It was between this, the biggest RPG series ever made and Tetris the most famous puzzle game. I prefered this.

Wii: SMG: Will go down in history as a classic.

PC - Half Life (theres a lot of great ones out there, but the modding / open ended multiplayer pushed it above the rest. Starcarft was certainly great, as well as Warcraft III and WOW (kinda recent). Ultima and Kings Quest VI, also DOOM, are mentionable)

SNES/SFcom - Final Fantasy VI (Honor.Men. - Crono Trigger)

Playstation - Hmmm, err, unnmm Final Fantasy Tact...ahh Metal Gear Solid. (Tough call really, but Metal Gear Solid was something else when it came up and I do believe it raised the bar big time.

Gamecube - Resident Evil

N64 - Masterpieces? kinda shy on this platform. A ton of good games but... I'd say Super Mario 64, it was groundbreaking. Goldeneye and Turok:Dinosaur Hunter are mentionable. more of a tie between Mario and Turok.

Genesis - Mortal Kombat

Dreamcast - Soul Calibur, Sonic Adventure, Guilty Gear, Shenmue, Ikaruga, NFL2K, Skies of Arcadia, theres just way too many to really go through. The list goes on.

NES - Super Mario Bros. 3
Game Boy - Tetris
SNES - Super Mario World 2: Yoshi's Island
N64 - The Legend Of Zelda: Ocarina Of Time
GBC - Pokemon Gold / Silver
GCN - Resident Evil 4

Atari VCS: Enduro

PC - Age of Empires 2

SNES - Donkey Kong Country 2

N64 - Super Smash Bros

Gamecube - Animal Crossing

PS2 - Only game I really enjoyed was Tony Hawks Pro Skater

Agreed on Blizzard, Valve, and id Software. For me though, old Westwood Studios PC games were masterpieces of similar cailber. Eye of the Beholder I & II, Lands of Lore, The Legend of Kyrandia, Dune II, Command & Conquer... for a long time, they were my favorite developer on any platform. Sadly, the quality of their games plummetted around the time they were acquired by Electronic Arts.

The Ocarina of Time
Majora's Mask
Okami
Shadow of the Colossus