Crisis Core- A great active time battle which makes excellent use of the materia system, it's A LOT more useful in this game than it is in FF7. With full control of zack being able to move him about ducking, dodging and blocking. The materia is easy to use and is set up to be used more strategically. It's a pretty solid hack n slash battle system which never gets old, especially with the DMW always spinning giving random bonuses and special abilities, keeps experiences fresh.
FF6- Every character was unique!! they all had their own signature abilities to go with all the magic spells they could learn. Each signature ability was useful in certain situations and added a good strategic edge to it. On top of that, the espers just made it one of the most effective battle systems of many RPG's. Anyone could equip any esper and learn any spell, allowing characters full customization making them be jack of all trades, masters of black magic, healers, ect.. on top of that espers also added stat and level bonuses to go with their summon abilities which varied from devastating attacks, to status inducing spell. This system was absolutely AMAZING for its time and still is quite a wonder.
Chrono Trigger- This can be simplified with 2 words, SIMPLE and FUN. Battles where not overly complex, enemies where seen on the world map and where fully animated sprites unlike FF's still pictures... With only 3 simple commands one would think it's nothing special but the tech system (which was also used in chrono cross)was AWESOME. Characters could perform attacks that varied which could hit one enemy or many depending on positioning on the playing field. To add onto that they could perform more advanced techs like dual and triple techs!! which allowed 2 or all 3 characters in your party to perform a devistating and not to mention really cool looking attack. it really gave a sense of team work between the characters, as if they were aware of each other unlike in other RPG's where they sometimes seem oblivious to their other allies.
Those are my top 3 battle systems that I thought where great, i would go on rambling about my other favs but I will just list the rest.
-FF tactics/ ogre battle games
-Zelda
-Golden Sun
-Legend on Dragoon
-Legend of legia
-Mega Man battle network games
and the list goes on...most systems are good in their own way, they tend to fit the game well most of the time.