Mentioned above, Azala from Chrono Trigger was awesome. He was so intelligent though not deeply developed due to short screen time. Lavos, the main villian, is quite fascinating, being a natural parasite.
Mitochondria Eve from Parasite Eve was pretty cool. I love the beginning of the game where(SPOILER) she just sets people on fire. It really got me into the game I was like, Whoa...I will say however I haven't finished the game just yet!
I'm somewhat ashamed to say I haven't played much of square's or enix's or squenix's games.