I totally agree with the first comment. Golden Sun (and its sequel, The Lost Age) are probably some of the best RPGs ever made ever.
Also, In agreement with another previous one, Tales of Symphonia and Tales of Vesperia are good too (and by good I mean Symphonia is THE best and most moving game I have ever played). However, I can also recommend more of the Tales of games, such as Tales of the Abyss, which comes dangerously close to Symphonia in awesomeness (it's for the PS2), and Tales of Phantasia for the GBA, which I lost so I can't say too much good about it. Also, Tales of Destiny is supposed to be pretty good. I haven't played it, though.
All I can say is that while the Tales of series are pretty much some of the best games ever, under any circumstances DO NOT PLAY TALES OF LEGENDIA. That is a very important sentence so I'm going to repeat it. DO NOT, UNDER ANY CIRCUMSTANCES, PLAY TALES OF LEGENDIA.
Also, with more games from Namco, I also recommend Baten Kaitos: Eternal Wings and the Lost Ocean (for the Gamecube). I quite liked it, though it's different battle system has been the subject of dispute.
Someone mentioned Star Ocean: Til the End Of Time. I would like to point out that, while it is a fantastic game and well worthy of recommendation (it's for the PS2, by the way), and the battle system is good, it is the most difficult game to level up in that I have ever seen. The battles take a long time and you don't get much experience from them, so make sure you fight a lot so you don't have to spend days tediously leveling up.