Pikachu. Everything, from its dumb clueless smile to its annoying ability which keeps me from using Body Slam/Return to kill it, there is not one redeeming feature about that thing.
Rattata and Raticate, but especially Joey's and the wild ones on Routes 225 and 226 in D/P/Pt who make it hard as heck to EV train b/c of crap like Endeavor and Super Fang...
Zubat, Tentacool, and Bidoof due to them being everywhere. This also applies to Rattata.
Pokemon with Roar, Whirlwind, etc. Stop dragging out Pokemon that I'm not trying to train at the moment, please.
WANDERING LEGENDARIES!!!