Objectively speaking, anything from Zelda II. But that game's too hard for its own good, so I'm not counting that for my own answer, especially considering I haven't ever been able to make it past the 3rd dungeon.
As for the hardest boss I've fought, I'm going with the final fights in SS. Oh, there are a lot of other bosses in other games that gave me a lot of trouble the first couple times through, but now I've learned their tricks and it's a simple matter of manipulating their own tactics against them. Not so with the final fights in SS. I've yet to come up with a good strategy against the horde battle, there's so many enemies rushing me on the screen at any time that it's really hard for me to keep my wits about me, and I get dog-piled a lot. Ghirahim, not quite so much, I mean yeah he's pretty hard, but I've gotten a good strategy now that doesn't put me at critical health. But Demise.... (shudder).... I have nothing. Nothing I try makes that fight any easier. Hell, even the Skyward Strike doesn't work with my strategy, by the time I get a lucky lightning strike he's already charged at me and knocked me down to half-health. He's far too aggressive for me to develop a strategy like every other boss. So I just go on the extreme defensive and hope I can get my health potions before he outright kills me. He still kicks my *** though.