Soul Calibur (DC)
Ninja Gaiden (Xbox)
Mass Effect 2
Halo
Jade Empire
Guardian Heroes
Eternal Darkness
Metroid Prime
King of Fighters
Brutal Legend
Rock Band

Bayonetta

Bully

Super smash bros brawl

Super mario galaxy

Paper mario

Paper mario TTYD

The world ends with you

Metal gear solid 3

Metal gear solid 2

Metal gear solid 1

Metal gear solid peace walker

Kingdom hearts 1

kingdom hearts 2

hmm I know i'll have to come back to this but I do want to put some things down now

Civilization 2 although I enjoyed the others and spinoff (haven't played much of 5 yet though) this one had by far the most hours of me playing any game.

The Lost Vikings

Super Mario Brothers 3

Sonic 2, 3 and Sonic and Knuckles

Master of Magic

Final fantasy X and XII

Okami

Bully

Shadow of the Colossus

God of War (whole series)

Baldurs Gate Dark Alience(sadly never played the pc ones)

Patapon 1 and 2

Ratchet and Cank Future

Uncharted

Infamous

still more to add but have to stop for now

1. Legend of Zelda: Ocarina of Time(N64)
2. Super Mario Bros 3
3. Skies of Arcadia: Legends(GC)
4. Metroid Prime Trilogy(Wii)
5. Super Mario RPG: Legend of teh Seven Stars (SNES)
6. Xenogears(PS1)
7. GoldenEye(N64)
8. New Super Mario Bros Wii
9. Metal Gear Solid 3: Snake Eater(PS2)
10. Warcraft 3(PC)
11. Tales of Symphonia(GC)
12. Diablo(PC) [I hate Diablo 2]
13. Final Fantasy VI
14. Duke Nukem 3D(PC)
15. Top Gear Rally (N64)

1. Legend of Zelda: ALttP

2. Final Fantasy VI

3. Super Metroid

4. Pokemon Heart Gold/Soul Silver

5. Shadow of the Colossus 

6. Super Mario Galaxy 2

7. Chrono Trigger

8. Ogre Battle 64

9. Final Fantasy IV DS

10. Tales of Symphonia

1. Final Fantasy VI (SNES)
2. Chrono Trigger (SNES)
3. Super Mario Bros. 3 (NES)
4. Secret of Mana (Seiken Densetsu II) (SNES)
5. Legend of Zelda: A Link to the Past (SNES)
6. Final Fantasy IV (SNES)
7. Legend of Zelda (NES)
8. Super Smash Bros (N64)
9. Zelda 2: Adventure of Link (NES)
10. Super Mario World (SNES)

I've probably forgotten some, but wow all my top 10 are shared between Square Co. Ltd. and Nintendo.

mario 3,castlevania SOTN,gta vice city,medal of honor frontline,cod mw2,the entire halo series. Those are the ones that stand out to me.

The Legend of Zelda: Majora's Mask

The Legend of Zelda: ALTTP

Resident Evil 4

Metroid Prime 2: Echoes

Final Fantasy X

Yoshi's Island

Castlevania Symphony of the Night

Metal Gear Solid 3

Fire Emblem

The Legend of Zelda: TP

1_ The Legend of Zelda: Ocarina of Time (N64)
2_ Donkey Kong Country (SNES)
3_ Final Fantasy X (PS2)
4_ Metal Gear Solid 2: Sons of Liberty (PS2)
5_ Goldeneye (N64)
6_ Counter Strike (PC)
7_ Soul Calibur (Dreamcast)
8_ Killer Instinct (Arcade)
9_ Metal Gear Solid 4 (PS3)
10_ God of War (PS2)
11_ Mario Kart 64 (N64)
12_ GTA 3 (PS2)
13_ Zone of the Enders 2: The Second Runner (PS2)
14_ Red Dead Redemption (PS3, Xbox360)
15_ Smash Bros (N64)

Just outside the list: Warcraft 3, Devil May Cry, Uncharted 2)

1) Shenmue 1 & 2;
2) Phantasy Star Online;
3) Zelda: a link to the past;
4) Super Mario World;
5) Sonic 2;
6) Sonic Adventure 1 & 2;
7) Age of Empires II;
8) Skies of Arcadia;
9) Grandia II;
10) Mass Effect 2.