Of the ones I own:

Tales of Symphonia is definitely my favourite. I have like 300 hours in my file (since you can keep your game clock when you start over).

Baten Kaitos is ok. The battle system is neat but it relies a little too heavily on luck for me. The story is pretty cool, too. It just suffers from bad pacing and godawful voice acting. I've heard Baten Kaitos Origins is better in all respects, but I haven't played it yet.

Skies of Arcadia is great, but my file got erased when I was like 10 hours in and I couldn't bring myself to start over so I don't have too much to say about it. Boo on evil little brothers.

Paper Mario: The Thousand Year Door is one of the best Game Cube games. The story is pretty much the same as every other Mario story, and there's kind of too much back tracking, but the writing is comedy gold and the battle system is superb. It's one of the few RPGs where you think "Gee, I wish there were more battles in this game."

Final Fantasy Crystal Chronicles is a lot of fun with more than one player, but kind of meh alone, and each player needs a Game Boy Advance and a GBA/GCN link cable to play multiplayer so it's not the easiest thing in the world to set up. If you're not going to be able to play with friends, you should probably skip this one. (Though the atmosphere and music are very well done.)

I'd say you can't really go wrong with Tales of Symphonia, Paper Mario, and probably Skies of Arcadia. Baten Kaitos is worth checking out, too, as is Final Fantasy Crystal Chronicles if you have everything you need to make it more fun.