Let's see, as for "villains" I didn't root for, I'll say...
The Frog Killer in the Muppet Moive- Because he's the only muppet bad guy (that I can think of anyway) that was ready and willing to actually kill Kermit. Granted this was a pretty small part of the movie, but that's still a WHOLE another level of evil my friends,
. Which of course, brings me to...
Doc Hopper- He didn't start off so bad with just wanting Kermit to be his mascot for his chain of frog leg joints, though pushy and annoying as not wanting to take Kermit's no for an answer. But after awhile, especially with hiring that frog killer, it was pretty much hey chill Doc.
Eddie Vrock/Vemon in Spider-Man 3- Not Vemon in the Spider-man comics and cartoons mind you, cause I thought the character was pretty cool in those. But in the movie, he was such a poorly written character that you can tell was just forced in there cause of his popularity in the comics. Some people I know also blame the actor that protrayed him, that being Topher Grace, but honestly I don't think it would of matter who they got to play him in that movie. I honestly think Topher did the best he could with what he was given so to speak.
Todd in Beavis and Butt-Head- He was just such a jerk and seemly got everything, including really hot girls, by being a huge jerk.
Maybe I'll be able to think of more later.
But as for baddies, I did root for...
I have to agree with everyone on Shedder and Krang.