I think Square was at their best 1993-1998. Secret of Mana, FFVI/VII, SD3, Chrono Trigger, Parasite Eve, FF Tactics, Einhander, Tobal 1-2, Evermore, Xenogears... tons of good stuff, and they really handled the 32bit transition seamlessly.
Enix was at their best 1990-1995. Actraiser 1-2, SoulBlazer, Illusion of Gaia, Terranigma, DQIV-VI, Robotrek, Ogre Battle... they really shined on SNES, but got a little lost afterward.
I'd say SE now is pretty disappointing by comparison, and really their only series that's held up imo is Dragon Quest.