Yeah when that ruby would punt players off your line it was maddening, made it pretty much a loss and forced me to many times say, "Well great, Gail." Emerald weapon was no slouch either but the tactics to beat him held up 100 times better. I remember the Temple Gate owning me a lot to while I was mid leveled in the story. Omega Weapon in FFVIII is a decent challenge as well as Ozma in IX. Belius, Ultima and Elidibus were pretty nasty in Tactics.
The final double boss fight on Ninja Gaiden was also maddening. If you died you had to start at the beginning of the stage. Drove me nuts and only actually beat that game a handful of times.
Battletoads was hard not because of the boss but the stupid vehicle levels. they were such horse shit, Turbo Tunnels, Volkmire's Inferno and Clinger Winger...
Top Gun - Landing on your own aircraft carrier was the hardest boss of all time.
I always had more trouble with Super Macho Man then I did Mike Tyson. I could never dodge the multi-spin punch enough times it seemed like.