pinnacle of turn based battle systems

The first two that come to mind are both PS1 games. Xenogears and Chrono Cross. Both games had somewhat unique turn based combat style.

From what I understand, Lost Oddessy has a pretty neat turn based battle style as well. Though I havent played it, so I wouldnt know personally.

SSI's silver box Krynn series, Battletech: The Crescent Hawk series, perhaps even Disgaea.

Honestly? Penny Arcade Adventures pretty much has the turn-based battle system down pat.