Wow this is like an impossible task.
1. Disgaea: Hour of Darkness (or Afternoon of Darkness)
2. All of the other Disgaea games
3. Dark Cloud II
4. Xenosaga (series. Second game is a ****pile, but the third more than makes up for it)
5. Tales of Symphonia
Honorable mentions, in no particular order:
Star Ocean: Till the End of Time; Final Fantasy VII; Final Fantasy VI; Fallout 3; Skyrim; Mass Effect series; Yggdra Union; Persona 3 FES; Persona 4; R-Type Command (the extent to which this is an RPG vs just a strategy game is debatable, but I'm putting it here for completion purposes); Knights in the Nightmare.
Reading this thread really makes me want to dig up my copy of FFVI, since I'm pretty sure if I played it now it would end up making the cut. Mostly because of Kefka.