I'll do an utterly personal list where no console game features since I only owned an xbox 360 for those 10 years and none of the ones I played would make a list.
1. Warcraft III, simply due to its custom maps. Primarily DotA.
2. Kana Little Sister, the game that made me love visual novels.
3. Battlefield Vietnam, the fps I've played the most. Averaged 5 play days a month for ~8 months.
4. Shogun: Total War, was a new experience in-between the older rts and 4x I had been playing prior. (Sad alpha centauri was to early.)
And there the list ended. I've played many other games I've liked and enjoyed in that time period, yet none has struck me enough to warrant a game of the decade label.

Was kind of a surprise for myself that no RPG warranted it in my mind since that is the genre I've played the most games in.