I'm a huge fan of the battle systems for (in no particular order):

Grandia: It felt like a more tactical look at the ATB system FF introduced.

Personas 3 and 4: Exploiting enemy weaknesses while defending your own is goven even more priority.

Valkyria Chronicles: More Strategy RPGs should adopt this format; it feels really smurfing good to have this sort of control over my units.

Vagrant Story: Chaining moves, and using defensive counter moves with RISK penalties, having individual body parts suffer from damage, all really clever.

Parasite Eve: I'm a huge fan of the first game's battle system, it has the same fun that action games poses when you have to analyze a boss's attack patterns to succeed.

Final Fantasy XII: I love the real-time model.

Valkyrie Profile: I love having to max the combo meter to chain together special attacks with different characters. The more ways I learn how to utilize character attacks, the more addicting it gets.

Tales Series: Used to be Abyss, my current favorite is Xillia. Xillia's AD skills are just so expansive and do so much for each character, I love it.

Chrono Cross: As much as I can't get into the game's story, I really like the complexity of its battle system. Although I'd probably pull my hair out when trying to get the game's good ending.