SotN/NitM galamoth -- no equipment
FF8 omega weapon -- level 99, all weapons downgraded to basic, no items
the mudman from megaman 1 NES -- no elec man trick
blaster master NES level 3 boss -- no grenade trick
the guardian legend NES final boss -- no subweapons
dragon spirit NES the 'decisive battle' with the orange/gold firey dragon type things at the last area -- no upgrades
contra NES the energy zone boss -- rifle (without dying)
ruby weapon -- no summon/gold saucer/northern cave materia
emerald weapon -- level 40 no KotR no final attack
ultemecia/griever succession -- no support commands unlocked
megaman 5 NES protoman castle final boss -- no stone man weapon (no he's not actually /that/ hard when you fight him, but he'd have kicked your ass without protoman)
willow NES -- second to last boss without equipped shield (I forget the guy's name, the one with the skull face)
final fantasy tactics -- stealing from elmdor without a mediator/oracle/temple knight (I know this isn't really a main part of considering the boss's difficulty, but YOU try stealing from him that way =p)
final fantasy tactics deep dungeon final boss -- no chantage or angel rings
jurassic park NES -- second level boss (rescuing the girl from the t-rex is a complete pain)
sonic 2 and knuckles -- final robotnik form (pretty difficult, maybe not hardest ever)
sonic CD race with metal sonic good future (not really a boss, and again not hardest ever, but fairly difficult if you get a good future there)
megaman 7 -- the greater majority of wily's castle bosses, no e-tanks
yeah I know the better portion of those are self handicapped, and aren't harder than things like I-no in GGXX hardest difficulty, but I figured I'd throw out some thoughts.
Final note -- the albatross from bionic commando NES with the original weapon (I don't know if that's possible as you may need to blow up a barricade when you first start with the proper weapon, but still)