OK, maybe I'll think about each villain out loud then cast my vote:
Doc Hopper - Very evil. Wanted Kermit to make money for his restaurant, hired a professional frog killer, and actually told the frog killer to kill Kermit.
Nicky Holliday - Evil. Got Miss Piggy into jail, tried to steal the Fabulous Baseball Diamond. Didn't try to kill a Muppet though.
Ebenezer Scrooge - Not really evil. He was mean, but then, he became nice. Have to feel bad for Scrooge. Everyone remembers the mean part of him. Sympathizing with the villain doesn't make him very evil.
Long John Silver - Very evil. Almost killed Captain Smallot and Benjamina Gunn, lied, tricked Jim Hawkins into giving him his crutch to take him along to the island for his compass, participated in a sword fight.
Rachael Bitterman - Pretty Evil. Tried to take over the Muppet Theater, even changed the contract to get it. Yet didn't really try to hurt anyone, though.
K. Edgar Singer - Not really that evil but more than Scrooge. Yes, he did take Gonzo, but everyone thought he was crazy, you kind of have to feel bad for him, like Scrooge.
Wiked Witch of the West - Haven't watch MWoO in a while, but I remember her being pretty evil.
Tex Richman - About Rachael Bitterman evil, but not quite. He tried to take over the Muppets in multiple ways. Actually, he and Bitterman are probably about equally evil.
And if no one minds I'll think about some non-mentioned ones on the poll:
Dr. Krassman - Evil. I believe he tried to kill one of the frogs.
Miss Finch - Not evil. Mostly just wanted to help Big Bird.
The Sleeze Brothers - Evil. Trying to make money off of Big Bird
OK, my decision (now that I've thought out loud way too long):
I can't decide between Doc Hopper and Long John Silver, as both tried to kill Muppets, but I'll vote Doc Hopper.