Hmm.. There's a lot.As I have only PS2,then...
1.)Dark Cloud 2 - Very innovative game.Cool story.Travels time to present and future to fix the natural order of time.
2.)Final Fantasy X - I don't have anything to say about this,because it is one of the greatest RPG game ever.
3.)Valkyrie Profile 2: Silmeria - Great gameplay,story.Although some will be confused with the storyline.
4.)Xenosaga Episode I: Der Wille zur Macht - Epic game.Cool gameplay,but character movement are rather slow.
5.)Xenosaga Episode II: Jenseits von Gut und Bose - Same as above.Except the gameplay getting worse.
6.)Xenosaga Episode III: Also Sprach Zarasthustra - Same as above,except better gameplay and graphics from the previous games.
7.)Wild Arms 3 - Great game,with wild wild west elements.An RPG with tough puzzles and great gameplay.
8.)Wild Arms Alter Code: F - A remake of the first Wild Arms game.Much better than the original counterpart,but long time Wild Arms fans does not like the game much.
9.)Star Ocean: Till the End of Time - A great game.Features real time battle like Kingdom Hearts,but must encounter enemies like FF games,although you can see the enemies are going.
10.)Kingdom Hearts - A superb game.Anti-Disney should avoid this game.
11.)Kingdom Hearts II - A better game than the previous one,with better gameplay and graphics.But the game is much easier than the first one.
12.)Shin Megami Tensei: Lucifer's Call - Features a unique battle system with demons as your friend.Dante will be the recruitable in this game.
13.)Shin Megami Tensei: Digital Devil Saga - Features a unique system with the Mantra system to learn skills (like Sphere Grid.).Anti-cannibals should not play this games,as demons are eating demons,while the demons are humans themselves.
14.)Shin Megami Tensei: Digital Devil Saga 2 - Same as previous game,but with a new Ring System to customize your party's stats.Great graphics.
15.)Shin Megami Tensei: Persona 3 - A superb game.RPG,dating sim,and etc are included.Probably has the longest normal playing hours,which are 60 hours or more as minimum.
16.)Shin Megami Tensei: Persona 3 FES - Same as before,but much better.With extra features,such as new difficulty and so on.
17.)Dot Hack (Infection,Outbreak,Mutation,Quarantine) - Nothing to say here,either.The games are great.
18.) Dot Hack GU (Rebirth,Reminisce,Redemption) - Nothing to say here too,as the games are great too.
19.) Radiata Stories - Good game,with same battle system like Star Ocean: Till the End of Time,except you can recruit more than 200 characters to your party.
20.)Suikoden III - Great game with great gameplay.You can recruit up to 108 characters,but not all playable.You can have 6 characters in your arty to battle.
I can't choose which game are the best,as each games have their pros and cons.PS1 have great RPG games too,but there is much more to list.I will list them down later.