My very favorite kind of all! - the Beast, who everyone thinks should be the bad guy, but he turns out to be the good guy.
Here's some other "antagonists" I've encountered recently:
- Physical handicaps. In The Window, by Jeanette Ingold, 15 year old Mandy survives a major accident but loses her sight
- Curses (or other dark forces). In A Curse as Dark as Gold, by Elizabeth Bunce, you get three different antagonists - but it's not clear until the very end which is the REAL bad guy or why, exactly, he's out to destroy Charlotte's mill and her family
- Tradition. In Lady in Waiting by Susan Meissner, Lady Jane Grey's main nemesis is the tradition of noble parents arranging the most politically and financially expedient betrothal
- Prejudice. Racism in The Help, by Kathryn Stockett (personified in Miss Hilly!)
- Nature. Surviving a plane crash in the wilderness in Hatchett, by Gary Paulsen
- Inner demons, like addictions or depression. In Revolution, by Jennifer Donnelly, Andi struggles with guilt, depression and drug abuse, feeling she's to blame for her brother's death.
- War. In Leviathan, by Scott Westerfeld, the conflict comes from the faceless opposing side. But when two teenagers from the opposing sides meet - you've got another one of those scenarios I love where the bad guys turn out to be the good guys
- Temptation. In Like Mandarin, by Kirsten Hubbard, Grace befriends a girl with a bad reputation (there are many other subtle "antagonists" going on in this story, too)
- Clash of culture, or values, or ideology: in Esperanza, by Pam Munoz Ryan, the young protagonist has to adjust to a new culture and way of life drastically different than how she was raised
- Institution/government: the Capitol in the Hunger Games series
- Difficulty communicating/misunderstanding: the basis of many literary novels
Late addition: just found this AMAZING article on antagonists by Kirsten Lamb (via Adventures in Children's Publishing blog) that goes into a lot more detail. A must read!