My personal top 5 in order:
1. Mass Effect 2 - i still feel like this is the best game i ever played. Mass Effect 3 diminishes my love for the series but the Suicide Mission of 2 was ill.
2. Persona 4 - my favorite PS2 RPG hell my favorite PS2 game. to me it mastered the Persona formula. Had a great cast, unpredictable story its followed closely by
3. Xenosaga Episode III: Also sprach Zarathustra - if only the whole series had the quality of this game. loved the ending even though there was little closure it still felt right.
4. Lunar Silver Star Story Complete - my favorite cast and villain of any RPG ever. also contains one of my favorite cut scenes in any game ever.
5 . Xenoblade - this game just gets insane plotwise as it goes on and keeps one upping itself all the way to its ending. a masterpiece and a love letter of RPGs to fans of the genre.
The Rest
6 . Lunar Eternal Blue
7. Chrono Trigger
8. Final Fantasy IX
9. Fallout 3
10. Illusion of Gaia
Honorable mention: Final Fantasy X