Dark Elf in Final Fantasy IV hardtype is an incredibly annoying boss since he's ultra-hard and you're forced into crap equipment through the path to him and the first half of him. I always dread that portion of the game when I'm playing the original hardtype version.

Another couple of bosses that have become some of my least favorite are Sanctuary Keeper and Seymour Omnis. Both of these are due to my Final Fantasy X No Sphere Grid/Initial Equipment/No Customization challenge attempt. Fighting Sanctuary Keeper hundreds of times a day, all day for about a week waiting for him to miss characters with evasion values of 5 will make you hate him. Seymour Omnis laughed in my face as he single-handedly ended my challenge making it impossible for me to progress at the very last stretch of the game.