For me in no particular order:
1. Cable and everyone from his timeline.
2. The Phoenix Force...I just loathe any story where it's a crucial plot point.
3. The O5 X-Men
4. Cassandra Nova...she was just a bad idea.
5. Left over Age of Apocalypse characters. It was a great story. I don't want to ever see any of them again.
6. X-23 (the concept just seems silly to me...always has)
7. The deaths of the original Generation X members. I always thought Skin's death was particularly unfair and depressing. He was just thrown out like trash.
8. Madelyne Pryor's descent into evil. I really didn't like that. She was made evil to justify Scott being a crappy husband who bails on his family. I liked Madelyne fine when she wasn't evil.
9. The slaughter of the Grey family at their family reunion. That was really f*cking depressing and I don't think I've ever been more disgusted with a story. The story even has Jean Grey's mother dying hating her daughter. Hate hate hate it.
10. Hope Summers
Honorable mention to other things I hate: Old Man Logan, that whole Revanche storyline, kid Apocalypse, anything third Summers brother related and Moira's death.
Of course death in superhero comics doesn't usually last, but it seems to be a particular joke in the X-Universe (Wasn't Siryn actually making fun of Banshee being dead because she thought that everyone else returns, so why not him?). I'm not sure if Reverend Stryker was supposed to be a mainstray in the regular 616 X-Universe, but there's really no point in bringing him back a million times. Also, get Lady Deathstrike some consistent characterization. She seems to go from being a villain, to a semi-villain, to an ally, to a FLAT-OUT EVIL villain, and then back again. I would also remove Apocalypse being retconned to so many characters as well.