i say gannondawf on ocarina of time

Metroid Prime for the Gamecube. It took me forever to beat Prime the first time. I even stopped playing the game for a little while, and then picked it up later. I don't think it would have been so hard except that that game was my first FPS.

Sephiroth in Kingdom Hearts 2 on Hard mode.

Deus in Xenogears (every time I died I had to go through the cut-scene which drove me crazy).

Killzone 2. Radic, elite mode. It took me over 300 tries to beat this level.

Spoilers;

Ooh, Shao Khan was pretty damn tough.

But I'm going with Mike Tyson.

alex trebec from jeopardy. although hes not a boss, its his game. i only managed to beat jeopardy once on snes with a lot of luck in final jeopardy. i think i won with a $2000 final prize range.

I dunno if it's the hardest boss battle I've ever beaten, but Brachyura from Castevania: Order of Ecclesia was as tough as nails.

I mean, I couldn't hit the Giant Enemy Crab's weak point for massive damage.

That crazy dude in Mario RPG (that's what me and my sister refer to him as because we don't know his actual name), but anyway he's in the town where you fight jinx, with those elemental diamonds.. I think he was in a square game. That dude took many long agonizing hours for me to finally beat.

sephiroth from KINGDOM HEARTS....

Quadraxis from Metroid Prime 2.  It took me over ten tries to beat it.