It really depends on what you look for in an RPG. If you like story-heavy games, the Xenosaga games are incredibly complex, beautifully crafted, and so deep your head might explode trying to wrap your head around everything. It's the Lost of RPGs, really, with more questions than answered but it answers what's important. The problem is the gameplay, what with hours of cutscene and maybe two or three hours of actual gameplay [And a hassle-filled combat system too].
If you like a blend of combat and storytelling, Bioware's games are pretty much the best. KOTOR 1 and 2, Mass Effect, and the upcoming Dragon Age are great examples of RPGs, and in my mind Bioware is my favorite RPG developer [Right next to Square-Enix].
My personal favorite, however, would have to be FF7. It's a classic, and was probably my first RPG.