FF6 and Chrono Trigger were by far the best RPGs given their time. FF4 and Secret of Mana are still worth playing. Lunar and Lunar 2 seem very obscure being Sega CD games, but they were well ahead of their time, and nearly flawless. Personally, I liked FF8 best out of the Square Soft Playstation games. Suikoden was pretty good overall as a series (Suikoden 3 had one of the best storyline concepts I've ever seen).
Before all computer RPGs became MMORPGs they had some great ones. Baldur's Gate 2 was fantastic, very old school Bard's Tale rocked when I was in middle school.