1. Beyond Good & Evil
A neat Zelda-esque cult hit with some cool gameplay mechanics involving photography and an interesting sci-fi story.
2. Shin Megami Tensei: Persona 3
While Persona 4 outshines Persona 3 in a lot of ways, I really enjoyed this game didn't want it to end. The story has a lot more weight to it and I grew fond of a lot of the characters. Definitely one of the best JRPGs I've played.
3. Freedom Fighters
One of the first great 3rd person shooters of the decade, this game innovated in a lot of ways with its, at the time, unique camera positioning and good squad based gameplay. The story was a little cheesy but a overall great game that should've received more attention than it got.
4. Radiata Stories
A action JRPG from the same vein as the Tales series, Radiata Stories most interesting feature was the amount of characters you could add to your party and the divergent storyline.
5. Xenosaga: Episode I - Der Wille zur Macht
The first in what was supposed to be a seven part epic, Xenosaga does the space opera better than any RPG before it. The story is completely wild with lots of twists and turns told through cutscenes that rival the Metal Gear series. While 2 and 3 don't capture the same magic that the first game did, Episode one is definitely worth a look.
6. Valkyria Chronicles
One of the most unique RPGs out there, Valkyria Chronicles mixes strategy, tactics, and 3rd person shooting in a fun and interesting way.