Any of the touhou bosses. And Tempest from Zone of the enders, I didn't know that you could target and shoot down the balls of fire he sent at you so i blocked all of them.
Gyorg in Majoras Mask is a pain in the ass. I hate how you would be trying to target him then bam omnomomomom.
Its been years since I played it, but there were some metroid prime bosses that kicked me in the dick.
The spider boss from metroid fusion
I can't think of any atm.
[editline]11:09AM[/editline]
Oh the final boss of Quake 4 was pretty difficult on the hardest settings.