#5 - Breath of Fire
Back in the prime of the SNES, Breath of Fire 1 and 2 were known to me and friends for little else than having a fantastic battle system. To this day, I remember little about the plots of the game, only remembering how much fun they were to play. When Breath of Fire 3 hit the Playstation, it brought with it a fantastic reinvisioned Breath of Fire system that kept the visceral qualities so important to the Breath of Fire feel, while adding in an interesting skill-copying system, compelling Dragon-Gene system that allowed you to pretty much custom build your hero for whatever enemy you were fighting, awesome master/apprentice system, surprisingly mature storyline for a game that stars children under 10 for most of the game, without ever feeling contrived, making it all-around one of the best games ever developed. Breath of Fire IV brought the system to perfection, adding the notion that your inactive party members were still involved in combat, and all-around tuning the engine into one of the best. Dragon Quarter... well, lets just say that while I did enjoy it, I hope BoF VI goes back to its roots.
#4 - Seiken Densetsu (Secret of Mana)
I refer to this by its Japanese name, because pretty much every one of the Mana games isn't named as a serial in the U.S. I'm sure we all remember the original Secret of Mana - truly one of the best games on the SNES. What Secret of Mana managed to do was wrap a great storyline in a consistantly entertaining action battle system, that set the bar at the time. While later iterations changed up the story-telling technique of the series, the battle system has remained reminiscent of the original for mostly the entire series (Dawn of Mana and Heroes of Mana notwithstanding). For those of us that played it, Secret of Mana 2 brought a number of excellent improvements to the engine, and I think it's fair to speak for the majority in saying that Mana combat reached its peak in the form of Legend of Mana. Legend of Mana was just fun to play, plain and simple, all the while providing a huge cast of characters, and an art style that only enhanced the gameplay experiance. I think most of the fans of the series are waiting for, at very least, Legend of Mana 2.
#3 - Final Fantasy
Some may argue differently, but I say the Final Fantasy Battle system has always been one of the things that defines RPG greatness for me. Reaching its first semblances of greatness in FFIV, Final Fantasy has evolved over the years, but has always, in my opinion, provided an improvement on the last iteration. Final Fantasy V brought classes back in a much more robust incarnation, while Final Fantasy VI traded classes for incredible character customization in the form of Relics and Magicite. VII evolved Magicite into Materia, adding a whole new level of customization, while again tuning the engine in almost every respect. Final Fantasy VIII took a curious turn, that paid off in the end with the Draw and Junction systems, along with a continuation of FFVII's Limit Break system, now a standard in the series. FFIX went back to the series roots with many things, simplifying character development in such a way that the game retained many of the modern improvements to the series while feeling decidedly old-school. FFX brought, as I mention later, the greatest turn system in and RPG to-date, as far as I'm concerned, while also introducing the sphere grid, and bringing back an improved version of FFVIII's weapon customization. FFX-2 was, and still is, my absolute favorite turn-based battle system. Dress spheres brought in-combat class changing, which I think is one of the best things ever. Any turn-based system that feels real-time enough to support a robust combo system is alright by me. Final Fantasy XII, while breaking away from the roots of the series in many ways, wasn't a total departure as many people imply - the liscense board was really just a evolution/combination of FFIX's skill learning system and FFX's garment grid. The only thing the battle system lost was turns, and I, for one, think it came out incredibly. FFXIII's already looking great.
If you ask me, Final Fantasy always gets it right. Not the best, necessarily, but definately among the greats.
#2 - Star Ocean
While the system has changed dramatically from the SNES game that, technically, no one here should have played, Star Ocean: Second Story on the PSX was for me, at the time, the pinnacle of RPG combat. It took the character development, menu driven spell casting and item use, and formations of more standard RPGs, and packaged them into a simply thrilling action battle system that, even after all these years, feels fresh and entertaining. Star Ocean: To the End of Time reinvisioned the system a bit, throwing a easy to understand, hard to master combo system, and streamlined skill activation, to produce some of the most cinematic, entertaining combat I've experianced in a video game, period. It's too bad that the rest of TtEoT didn't live up to the Star Ocean experiance, but you can bet I'll be preordering Star Ocean 4 the moment I can. (Also, the first two star ocean games are being remade with an enhanced Star Ocean: Second Story engine for the PSP! I'll so be there. Let's hope they do a bit better with the voices, even though the old ones did grow on me...)
#1 - Grandia
Grandia games always provide this fantasic, visceral experiance. The way the animation and sound effects are done make the attacks sound powerful in a way not many games get right. This is on top of what I think is the best turn-management system ever (FFX being a close second), great options (you can just kill the boss, or you can destroy his arms, first, and get better items, money, and experiance!), great skill learning systems, and all around great fun. Grandia III, while getting closer to living up to Grandia's pedigree than Grandia II, still fell short - but contains the greatest iteration of the Grandia system to-date. You can bet I'll buy Grandia IV.
Runners up/Honorable Mentions -
Lufia 2 (if you include the dungeon mechanics, as well)
Xenogears
Radiata Stories (Radiata Stories was made with a simplified version of the Star Ocean III engine, not Grandia)
Tales of Symphona/the Abyss
Xenosaga III
Brave Fencer Musashi
Alundra