My very least favorite is Kingdra, because I think it looks drunk, is stupidly lucky, ruined a cool Pok?mon (Seadra), doesn't deserve to be a Dragon-type and a ton of other things.
Other least favorites, to quote myself from my own forums:
Gulpin: It's a blob with a disturbing mouth.
Umbreon: I've had Umbreon fans up my nose very often for not liking it, so I've grown to like it even less. Colosseum kinda made up for it, though, because I always get attached to the Pok?mon in my team...
Shroomish: It's got a rather ugly face to my opinion, and additionally it's a blob with legs but no arms.
Blaziken: I think it's horribly ugly and seeing people with "BLAZIKEN ISH TEH R0x0rz!!!!!one" in their signatures all over just annoys me.
Snubbull: It's wearing a pink dress...
Skiploom: The face combined with the ears is just very unattractive to me.
Azumarill: I just started realizing that it was Azumarill I should be disliking, not Marill. Basically, it's egg-shaped with long ears...
Crobat: I just think it's kinda ugly.
Regice: Ballerina ice cube...
Snorlax: If you NetBattle, you'll get a grudge against it, trust me.
Igglybuff: It's just... not cute.
But I don't hate any Pok?mon. Not anymore. I used to hate Kingdra, but I haven't been to the Crystal Battle Tower for a while, and that's the main reason I started hating it.