Seriously the only ones that gave me trouble were Gannon from LOZ and Ganondorf/Ganon from TP. Seems pretty random based on what everyone else is saying but those were the only challenging ones for me. I do have to note that I abused the corner against Dark Link and used the Fierce Deity's Mask against Majora (for the first playthrough at least) so while I acknowledge that they are probably the two hardest, my experience fighting them was extremely easy due to the tactics I used. In retrospect I could have also used the fishing rod trick in TP to make the fight easier, but I had no idea that worked when I first played through the game.
Also I wouldn't consider going in the corner against Dark Link to be cheating because there's no rule that you have to be on the offensive when you fight him. The player being passive is his achille's heel just as virtually every other Zelda boss has a weakness. I would say that his particular weakness is probably more likely due to a flaw in programming than intended by the game designers, but it did make it into the final version of the game. I understand if you consider it cheating within your own playing of the game, but it's not like Nintendo declared "Oh by the way we screwed up so don't go into the corner against Dark Link because it's cheating." I do agree though that with that caveat of not going into the corner he is the hardest. However if you get into caveats then there's nothing stopping me from saying Ganon from OOT is the hardest boss if you wear the iron boots the whole time and only allow yourself to use the megaton hammer and master sword for only the final hit.
Keep in mind I don't really believe all this and I'm more just playing devil's advocate. I do think it being cheating is a bit of a stretch though.
