I generally find Homestuck to be the most annoying. Nothing like getting glomped by people covered in paint. Please, please, please, have some self awareness. I know I'm tall and all, and thus can withstand your tacklehugs, but I really don't want paint on my cosplay. I also, and this isn't really a strike against the fandom itself, find homestuck to be very visually uninspiring. I've seen a *few* impressive homestuck cosplays, but generally it's a drab ocean of t-shirts, bodypaint, and horns.
Hetalia would be a second. I know it's relatively isolated incidents, but there have been some things done by the fandom in staggeringly bad taste.
MLP, well, actually doesn't bother me. It's got some immature members, like any other fandom, but the message they're about (friendship and tolerance) is a good one, and I think men getting into a "girls" show has done more for combating gender preconceptions and stereotypes than years and years of trying to get girls into "guy" things. I've also seen the fandom raise a lot of money for charity (things like children's hospitals), which is always an A+ in my book.
"The important thing is no one was hurt... No one who counts."