Xenogears for the PS1 had one of the best combat systems I've ever played. Tied with Star Ocean 2 for the PS1. There's a remake which I think they overhauled the combat system, so I'm not sure if it still is as good as the first edition, but the customizability was amazing.

After that Grandia was fun, but I played it far less than the aforementioned, so have less to say. Chrono Trigger was very good for what it was, and IMHO was only matched by FF6 in that category (heavy turn based combat systems). Chrono Cross is an honorable mention in that category as well.

Lastly, very recently the Sea of Stars game had a very good combat system.

Ultimately these games have great stories, and that's all I really cared about, but the combat systems could either make or break the monotonous grind to get to the plot points, so they had to be at least decent to make the games playable.

I highly recommend any of these games. Chrono Trigger in particular is highly regarded as possibly the greatest JRPG of all time, and personally I'd put Xenogears at 2nd place, with Star Ocean 2 at 3rd. But I might just be nostalgic.