Well nowadays as my skills have increased I don't really think many bosses are too difficult anymore...
But I think one of the most difficult bosses I've ever fought, wasn't even the final boss of the game, and everyone I've ever heard who has played this game is mostly unanimous on declaring him the hardest boss... is Boost Guardian from Metroid Prime 2 Echoes. It's only in the second area, towards the beginning of the game still! No light crystals, hardly any energy units, and this fast mother fucker shooting around while you constantly lose health. Go to hell Boost Guardian. When I first played Echoes I quit playing the game for almost a year because I could never beat this guy.
Zombies have appeared!
You take action: >Fetch Musket
You just got Koopwnd™!