Magus was a breeze.
As was Lavos, if you actually bothered to complete all the side quests.
Queen Zeal at the end of the black omen, though, she was fucking hard.
Dark Link in OOT was just fun. In fact, I wish that game had a 2-player battle mode (preferably one which doesn't allow the use of shields) so you could have battles like that whenever.
The Axem rangers in SMRPG owned my ass the first 20348752093578 times I fought them.