The 2000s was the time I slowly fell off gaming as I did in the 90s. I came not back until the Wii roped me back in. But for 2000 I still played some of these games. Mostly the sequels: Baldur's Gate II, Diablo II. Another great game and probably underappreciated gem is American McGee's Alice. Majora's Mask I only played many years later once I was back into gaming and on console for the first time.
Anyways, I am going with Diablo II here, it improved the formula more than BGII and was overall a really fun game. Sadly I feel it lost a bit of the atmosphere of the first game, but I think more than the first game Diablo II is the blueprint for the genre with many, many games we see still until today.