I am honestly very surprised with this result. I found Moldorm very easy to defeat by quickly maneuvering around only using spin attacks. If I recall correctly, the damage between falls from the top level are still in effect when you get back to the top. Sure, he can a little annoying the first couple times you fight him, but when you revisit the game, he's not really a boss that strikes me as hard.
Mothula could be frustrating if you went in with low health, but it's really a matter of being prepared in that fight.
Some of the harder bosses I would say are the Helmasaur King, who hits like a truck very early on in the game with an attack that is excruciatingly hard to dodge (a very precise sword attack that deflects you out of range). Vitreous, who I voted for, is a boss fight that requires you to pay attention to many things at once, and requires Punch-Out-like observational skills to be able to ascertain when and where he's going to be able to do a lightning strike; I still die on that boss when I replay the game, and usually more than once.
Well, Ganon goes without saying, so I'll keep my vote for Vitreous.