My all time favorite Disney villain would have to be "Scar" from the Lion King. Jeremy Irons absolutely made this character come to life.
Second place would have to go to an old time villain named "Pete." This character has been a nemises for Mickey, Donald, Goofy, and many others. He has played many tough roles over the years from a salesperson to a mean boss, and even a nasty neighbor. But my favorite role he played was when he was the "Ghost of Christmas Future" in Mickeys Christmas Carol.
And lastly, honorable mention would have to go to "Commodore Barbossa" in the Pirates of the Caribbean. I think he was a great complement to Captain Jack Sparrow as his nemises.