Baldurs Gate 1,2

great overview, complete control over six characters and you can time it differently depending on the battle... kill little goblins in real time in seconds and take a half an hour for the hard battles... the game just had a perfect flow and the level of control over the battlefield was just brilliant...

^ Good choice, but that's my second.
Diablo II.

Just point and click, that's all you needed to do yet it was beyond satisfying and when fighting other players you really had to have some serious poitn and click skills to hold your own.

I also enjoyed the legend of the dragoon battle system with the timing, but it really can't hold a candle to Diablo II's.

I like the Tales of Vesperia battle system above all others. It's the best and deepest action system I've played.

The second game is Vagrant Story.

Third is FFVIII.

Fourth Secret of Mana.

Fifth, Fallout 1/2

If you don't count Deus Ex then I'd choose Panzer Dragoon Saga.

Baldur's Gate 1/2 has a really nice battle system. the ability to zerg fast if you wanted (and were strong enough) and also the ability to plan out your fights (pause feature), made for a good balance where you never felt rushed even in hard battles.

Diablo 's was a satisfaction combat system, you could just go out and destroy stuff and have tons of fun doing it, its combat system really matched the way you could build your characters perfectly..

for Turned based rpgs, I really digged FF10's battle system. FF4/Chronotrigger's Active combat system was great but with FF10 you could really properly plan the order of attacks (since it showed up on the side, including the monster's attack), and see just precisely the advanges you would of got using specific characters to attack at specific times..

I would have to agree with the Chrono Triger battle system. i love turn based RPG's

Star Ocean: Til the End of Time had probably my favorite battle system.

Secret of Mana was great as well.

At the same time, I'm a huge proponent of turn-based battles, such as Crono Trigger and FFVII.

The first Xenosaga.

The best one ever is of course FF VII... it's impossible to outdo such a flexible system.

The 2nd best is Star Ocean 3 (Star Ocean: Till The End of Time)...

3rd... probably Chrono Trigger.

I'm fond of Dragon Quest 6's system, mostly because it was the first RPG I ever played and I liked the job system.

Recently, I've liked more real time battle systems. Mass Effect and Oblivion were fun, but they had their problems. Fable was really fun when I became a super evil, super powerful magic guy. Lost Odyssey was fun in the beginning, but now it seems tedious.