Okay, this is my interpretation of your question.
You go into a diamond store, all the diamonds in there are incredibly good looking and well worth the price, and each and every one of them is absolutely beautiful in its own way. Now pick your favorite.
Pick a favorite out of...
Secret of Mana
Lufia 2
Earthbound
Final Fantasy 4
Final Fantasy 5
Final Fantasy 6
Chrono Trigger
Zelda: LttP (if you call it a RPG, I call it an adventure game)
How the hell are you supposed to pick from all these???? Lufia had the greatest puzzles I've ever seen in a video game. Chrono Trigger was, well, fucking Chrono Trigger. FF4 laid down the framework for all JRPGs to come. FF5 gave us the job system, which allows for nearly endless character customization options. It does have the drawback that to even have a chance of getting through the game you have to spend a ridiculous amount of time leveling up and training. FF6 had an amazing story, wonderful characters, a wonderful esper system, and the world of ruin was so incredibly open ended and so much fun to explore. Zelda: LttP was one of the best games in the best ever series of games. Secret of Mana was, well, fucking Secret of Mana. Earthbound was so damn quirky and funny and entertaining.
That all being said, I suppose I'd have to go with FF6 as the best of the best. It's was long, open ended, never felt like it was dragging, had the best story of all the games I mentioned, a villain that still gives me nightmares, had it's funny moments (Ultros!), and had a very decent amount of hidden goodies. Definitely one of my favorite games of all time. I never quite understood the zealous-like admiration that so many people have for Chrono Trigger. The game was great, but I don't really consider it on the same level as FF6 or 7, mostly because the future world blew so much. If you haven't played Lufia 2, PLAY IT NOW! FF4 had a story that never really caught on with me, and 5, punishes you mercilessly for trying to just play the game without obnoxious amounts of training.
Point being, all these games are great, FF6 being the greatest. No system since the SNES has had this many good RPGs worth playing long after the newer systems have come out. Let us rejoice in the glory that was mid-90's console RPGs.