I'm not sure if I'm supposed to post bosses I hate because they were written as cunts, or bosses I hate because they were headbashingly difficult, or bosses I like because they were just memorable. So...
Knight-Commander Meredith (Dragon Age 2): DA2 had quite a bit of flaws, but it also had extremely memorable characters, including Knight-Commander Meredith, leader of the Templars in Kirkwall. Of course, depending on your point of view, she could be your hero (you mage hating monster), but when even most of her fellow Templars thinks her methods are too extreme, then you have queen bitch.
Zhao Yun Ru (Deus Ex: Human Revolution): Sly, manipulative, and power hungry, Zhao Yun Ru owns Tai Yong Medical, one of the world's leading augmentation companies. Of course, if she had it her way, she'd own the world's only augmentation company.
Ahriman (Prince of Persia 2008): It's amazing how a make a simple platforming sequence awesome. (WARNING: Massive spoiler after 6:00)
Izanami (Persona 4): Yeah, fuck you. Entire dungeon in just a single day and you being ridiculously difficult? Two raised middle fingers from me.
Alatheia (Trauma Center: Under the Knife 2): Fuck you too. I have never wanted to stab my DS more.
Ops and Brachion (Trauma Center: New Blood): The two strains of Stigma that were pretty much designed with co-op in mind, and are very very annoying to manage on your own.
Dark Bowser (Mario and Luigi: Bowser's Inside Story): This is mostly for the and the background setting.
Ice Magic Beast (Lost Odyssey): AKA "the boss at the end of Disc 3" or in my case, "the boss you will have lots of 'fun' with if you completely ignored Mack throughout the game," given that he is the only character that can damage it.
Okay, so my definition of "one" may be skewed, but... shut up.
