Did someone say mini-boss?
My all-time hardest minibosses:
Culex and Jinx, SMRPG
Son of Sun and Mother Brain, Chrono Trigger
Those are all I can think of (right now), but I'm sure there are others. Reasons for each on the list (which may or may not grow):
Culex is hard because of all those crystals. Each having a different weakness, and a different element, plus Culex's shadow-type magic--I always think of neutral element magic as shadow type--means you almost NEED Princess Peach in your party just to stay in the fight.
Jinx is on there because of that damn Silver Bullet. How many times I've lost to that I'll never be able to keep track of. I think it's somewhere around 50 times or something...*AHEM*
Son of Sun...This miniboss drives me nuts. Have to find the right spheroid satellite thingy in order to damage it, or you get your ass kicked. Plus it changes the position of the spheres.
Mother Brain. Similar name, different concept. And oh, let's not forget that it can recover 999 HP when the monitor heals it, besides the fact that if you take the monitors out, you get smacked with a powerful beam that wipes out half your HP with one blow (just so you're all aware, I've never had more than 500 HP with any character. High defense power is a must).
Squaresoft's game designers may be losing their touch, but I'm sure there's still a few annoying yet rewarding sidequests left in their system.