I hated most of the bosses in SS so its hard to choose just one.
I hate the Imprisoned and he just gets more frustrating with each fight. Especially if you down him then can't run passed him and need to drop down to another level find a geyser then fly back up, run over to him and pray you aren't too late. Also the one chance and if you fail you're screwed part of the final battle when you have to launch link onto its head... i hated that too.
I hated Koloktus too because he was such a chore, he moved so slowly and took so long to start and finish attacks that it just made me feel so bored. The worst part for me in that battle is when he finally stands up and you have to wait for him to stop swinging his swords around, he isn't a threat if you keep your distance and it really isn't hard to do that so its just a bore-fest until he stops. The constant pulling himself together was annoying too, the battle seemed to the half preparation cutscene and half a battle...
I don't like Tentalus either because not only does it look pathetic, its screws around like Koloktus too much, i hate having to deal with its tentacles that pop up through the ship's floor, it doesn't even make that much of a difference if you hit them or not. I also hated hitting him in his eye with the bow, though i hate him less then the other two because i do like rofl-waggling the wiimote to cut down the tentacles it sends flying at you in the second half of the battle its perhaps the least boring phase of a boss in the entire game.