Little late, but finally in to comment. Great to see GTA: SA so high. That one gets my vote for best of the series, since it was just the right blend of story/character and wacky world/play mechanics (jetpacks in gang turf wars! It's so simple!). Then there's Silent Hill 2, which is about as close to a playable nightmare as I've ever seen.
As for Bioshock, well, that game was pretty flawless for me, and also (almost coincidentally) marked something of the point of decline in my general gaming lifestyle. Not in the sense of any fault of the game, just that this was also a point in my life where my general priorities started to shift, and this was the last game that I was well and truly obsessed with to the degree that I was. And still am a little bit, though (I was much kinder to Bioshock 2 than most, if only because it was another trip down to Rapture).
Anywho, time for my list:
1. Bioshock
2. Manhunt
3. The Legend of Zelda: Majora’s Mask
4. Psychonauts
5. Silent Hill 2
6. Grand Theft Auto: San Andreas
7. Rise of Nations
8. Advance Wars: Dual Strike
9. Timesplitters: Future Perfect
10. RollerCoaster Tycoon 2
11. Halo 2
12. The Legend of Zelda: The Minish Cap
13. Mass Effect
14. F.E.A.R.
15. Dead Rising
16. Splinter Cell: Chaos Theory
17. SSX 3
18. Jet Set Radio Future
19. Burnout 3: Takedown
20. Resident Evil 4
21. Hitman: Blood Money
22. Pikmin 2
23. Luigi’s Mansion
24. Eternal Darkness: Sanity’s Requiem
25. Dead Space
Looking over it, while there are a few that I could easily have omitted for the ones I forgot (KOTOR! Shadow of the Colossus! Freaking Paper Mario!), there are still a couple that I'm surprised never made the list. JSRF came with every new Xbox for a while, which was good, since it gave everyone a chance to experience that awesomely enjoyable game for themselves. And no Psychonauts? That's easily one of the finest platformers ever made, one who's goofy humor, art design, and general playstyle still strikes a chord as incredibly original. For those who haven't yet played it, please do give it a go, you won't be disappointed.
Still a great list overall, of course (thank you Pak for running it!). The way I look at it, there were simply too many amazing games in that decade, so even with so many of my personal favorites not included, it still ended up being a fantastic collection here. Good stuff.