A list from me:
Pinkamina (the serial killer) - So many gory fanfics about this, it's quite excessive.
Princess Luna - Most of her fans are way too obsessed with her to the point where it gets silly.
Vinyl Scratch - Too many people are overly obsessed with her because she is a raver/DJ.
Derpy (or Muffins now) - Ever since that controversy of that character getting removed from the show sparked, the popularity level was through the atmosphere and you couldn't go a day without seeing Derpy material. Luckily this is starting dwindle.
Dr. Hooves - I don't know about the rest of you, but this character is seriously annoying. Plus Dr. Who fans are overly obsessed with him and never seem to stop talking about him that I've noticed.
Fluttershy - The vast majority of her fanbase is way too obsessed with her, I dare say even worse than any other character in the show. Write a short story that makes Fluttershy cry and see where it leads...
Shipping - The idea around it can be fun, but people take this sort of thing WAY too seriously.