Yay, large list:
Cave Pokemon
Zubat: Not only is its leech life and confuse ray so annoying, its cry doesn't help :\ Also, IT'S IN EVERY SINGLE GAME!
Geodude: Similar reasons to Zubat.
Route Pokemon
Ratatata: I hate Raticate and Ratata :\ Not only that, when I'm searching for a Pidgey 'A wild Ratata appeared :\'
Weedle: the ugly, worthless version of Caterpie :\ Honestly, its Poison Sting is annoying like hell when you first start the game :\
Hoot-Hoot: I dont mind Sentret, so I had to pick on something :)
I like Zigzagoon and Poocyhena so Im not going to pick on them :)
Bidoof: Bidoof...Bidoof...Bidoof! Honestly, its cry sounds annoying! It looks annoying! It is annoying! Nuff' said.
Water/Sea
Tentacool/cruel: This Pokemon was just made to be hated. If I'm correct it appears in every game! Wrapping you and poisoning you! Also, it is like the only pokemon you find :\