I never imagined that this would be what finally convinced me to sign up, but I guess I don't know myself as well as I thought. Going through the list on Wikipedia, I have realised that a lot of games I first thought of were actually from 1990-1999. That was quite a revelation for me, but I persevered and here's my list:
2000: Legend of Zelda - Majora's Mask This was a hard choice, especially since my runner-up seems to also be a slightly underliked part of a franchise. (That runner-up would be Final Fantasy IX by the way).
2001: Legend of Zelda - Oracle of Seasons/Age These games took up a lot of my time, but otherwise it was quite a dry year for me (I didn't play many games in 2001 apparently) so I have no runner-up.
2002: Ratchet & Clank Awesome game, I wish I still had a PS2 to play it on. Compared to 2001, for me 2002 had far too many good games in it. My runner-up is Super Smash Brothers Melee, but honourable mentiosn must go to GTA: Vice City, LoZ: WindWaker and Metroid Prime.
2003: Command & Conquer: Generals My introduction to RTS, this game helped me realise that I was no good at RTS but enjoyed the genre anyway. My runner up for 2003 is Primal, and I can't help but give an honourable mention to Mario Kart: Double Dash since I'd pick it over the Wii version anyday.
2004: Evil Genius Took far too many hours of my life, but who doesn't dream of managing a base of goons and threatening to turn off gravity if the world will not cave to your demands? My runner-up was Half-Life 2, because while it's a great game in my opinion Evil Genius trumps it.
2005: Guild Wars Over 800 hours played in the last year. That's a scary number to me, but at least that was 800 hours of fun. My runner-up is Truama Centre: Under the Knife, which I never finshed as I am still stuck on Savato(I think that's the name), the final level in the main game. Honourable mention to Resident Evil 4 (although I didn;t play it until Wii release).
2006: Dawn of War: Dark Crusade Best game I played in 2006 (apparently another drought year for me) and really enjoyed. My runner-up goes to The Godfather: The Game.
2007: Team Fortress 2 Got it in the Orange Box, but I think the game itself deserves the title instead of the Orange Box. Not because the other games were anything but excellent, but that I feel that multiple games shouldn't take the title. My runner-up is Crackdown, and an honourable mention to LoZ: Phantom Hourglass.
2008: Rock Band Although the priceiest game on the list, the money was well worth the improvements over Guitar Hero for it's multiplayer. When I'm home from University, me and my Highschool friends still occassionally get together and play. The runner-up this year is Left 4 Dead.
2009: Minecraft It has been a rough year in gaming for me, due to a lack of funds (being a student sucks, moneywise). Minecraft is a sandbox builder game, but it is so much fun for the price (free at the moment since it is in public alpha). My runner up is another small game, Plants vs Zombies which has provided cheap entertainment in a year so worried with finances.
Out of my choices, I'm going to say Ratchet & Clank.
Wow, I didn't realise that I would write so much, so I bolded the games and year for your conveinence.