I think the system used in Chrono Trigger is great, I guess technically it's just the ATB system, but the harsh timing really requires you to think on your feet as you're planning your attacks. It blends the tension of an action game with the thoughtfulness of a turn based combat system. It doesn't hurt that all of the bosses are so well designed either.
Pokemon has a really clever little battle system. It's simplicity is really it's greatest virtue, and for the sake of this simplicity they made a system that isn't quite like anything else. It's also the only system that I think works really well in a multiplayer setting.
The Bravely Default system has been really refreshing as well. Normally I find systems like the one in BD really repetitive and slow paced. The Brave system totally destroys the repetition though, and that paired with the song based buffs makes the combat move a hell of a lot faster.
The systems in Persona 3 and 4 are pretty great too, though I've never really been able to articulate what I like about them. I'd include stuff like Fire Emblem, Final Fantasy Tactics, and Tactics Ogre, but I'd consider those more strategy games than rpgs.