1. Crusader Kings II (with all the DLCs) - IMO the greatest RPG of all time, the level of character depth in this game is unbeatable, you can basically build/take a character from scratch and turn him/her into anything you want, thus creating your own story, the choices are practically endless.
2. Fallout 2 - IMO the best in the franchise, Fallout 2 did everything better than what FO 1 did.
3. Baldur's Gate 2 - The quintessential RPG of the early 2000s.
4. Planescape: Torment - IMO the storytelling in this game is unmatched even in today standards
5. Darklands - Darklands is a great adventure and is certainly one of the best multicharacter RPGs in the 90's, for a game from 1992, its well-drawn graphics, multiple quests, good character generation, and flexibility in play, the game's detail is phenomenal.
Legend of Legaia
Mass Effect 2