Best Villian: Long John Silver! He is scary and sneaky, but you can't help but love him. Also, his laugh is amazing. So evil and cool.
Next would have to be Joan Cusack from VMMCM, because she did an excellent job. For a tv movie, VMMCM is so well done, and she's just really good at being mean.
Then comes Nicky Holiday, just because he's really suave, and for a movie that is very MGM-style musical, he does a really good job. Plus he's not hard on the eyes.
Next would be Doc Hopper. As Vic stated, yes he did want to kill the frog, but I personally found him a bit annoying rather than evil. Maybe it's just because the first time I saw TMM movie I was in my teens, but the first time I saw MTI was in theatres when it originally came out, when I was a bit younger.
It's hard for me to consider Scrooge a villian, just because he is the protagonist as well, but if I counted him, I'd fit him in between Joan Cusack and Nicky Holiday.
Edit: Anyone else notice that Lady Holiday is british but her brother is not? That always bothered me!