Super Mario Galaxy

For me...

#1: Resident Evil 4

The pinnacle of video games as a medium in my opinion. From it's pulse-pounding action, to its perfect pacing, to its incredible boss fights, to its atmosphere and audio-visual design, it's simply a masterpiece in every way.

#2: Super Mario Galaxy

The perfect blend of insanely polished gameplay and pure childlike wonder. It's like they distilled happiness into video game form.

#3 Bioshock

A tour de force in atmosphere and storytelling, set in an unforgettable world and galvanized by its superb plasmid-powered combat.

Tales of Symphonia BAYBEEEEEEH

The perfectest of RPGs, the bestest characters with the bestest story.

Both a very important game for me growing up and one that I give some time to replay whenever I can, just to reconfirm to myself that this is for me, at the top of the genre.

The whole experience still makes me feel the same emotions as that first time, if not stronger at times, its pacing, level design, the sheer fun of the combat system, simple yet effective, its artstyle, memorable soundtrack and excellent dub that no other JRPG can even come close to compare, is just a really excellent game.

Metroid Prime as an overall game, but a tie with RE4 and HL2 in terms of impact.

God of War 2 obviously.....

Baldur's Gate II - sure, it's not as good as pen&paper D&D experience, but, beside Planescape: Torment (1999), probably closest a video game ever got to it...so far, at least.

GOW3

Metal Gear Solid 2. There are some aspect in it that I've grown to not like as much as I used to, but I think it's still an excellent game, and most importantly, it's more relevant than even with its themes regarding society.

The decade had other excellent games as well. Final Fantasy X is another one that always seem to rival Metal Gear Solid 2, but other titles dear to me include Wolfenstein: Enemy Territory and Titan Quest.

That's a 2010 game, so it's not part of the 00s.