I agree with most of these (lol and M&L RPG 3's US title: Bowser's Inside Story!), but I'm adding Chrono Cross to the list, if that's okay. I just beat it, and although the Element and Stamina systems are confusing at first, they're very simple once you get the hang of it. And for clarification's sake, it's for the PS1. Also, Radius' explanation in-game at the beginning of the game helps immensely (go left after leaving your house! He's the old guy).
EDIT: Sorry, for this console era, M&L RPG 3, and all those other DS ones mentioned. Missed that comment, sorry Ares.