Of course one can always point to something like Chrono Trigger and say it is great because it is, no doubt about it. However, I've always been one to find more joy in the little things.
First off, one of my favorite additions to any turn-based combat system is Disgaea. Aside from making almost any level a tricky puzzle on how to clear the level doing the most damage to the geopanels, it also had the super-entertaining lift/throw system that was a constant amusement, especially if you have a few penguins lying around, and the combos and spells that you could access even from the beginning felt unique.
OK, that turned out to be more about the game necessarily than the turn basedness, but lets look at another one that always amused me, Chrono Cross. While it has some bits that definitely detract from the finished product, I was always pleased with the way you were forced to manage your spells carefully. The limitation made me choose a lot more carefully when I fought and led to more time spent with those spells customizing than with Materia. Which, unfortunately, turned out to be my downfall as I have never finished the game. I spent so much time and just barely had made it past the halfway point. The balance of magic in that game was always one of my favorite points of it though, so a plus there.
Golden Sun was another great example. Every move changes the way you have to play the game, as you can change classes mid battle if you plan it right. The summons were something you had to plan in advance since even getting them would often leave you rather weakened, and the creatures themselves were charming without being cute and annoying. The Djinni are the unique bit here, and they were what made the game special to me.
