I like the reasoning some are giving for Ted DiBiase as The Million Dollar Man not being cheered -- and I'd say he'd definitely be a top contender. However, DiBiase didn't really participate in an era where heels really became "cool". I think if he had lasted, he would've been right there with guys like Flair, Savage, and Rude.
Speaking of those three, I consider Flair, Savage, and Rude the best heels of all time at least from the time that I remember wrestling. I can't speak on guys like Gorgeous George, Hans Schmidt, Freddie Blassie or The Sheik who I'm gonna take a guess someone could make a strong argument for them setting down the roots of what makes a great heel.
To me, Randy Savage takes the prize though. His run with Miss Elizabeth and his pairing with Sensational Sherri just exudes nastiness, paranoia, and that over the top wrestling persona that just seems positively crazy. Due credit to Elizabeth for playing the damsel in distress who can't condone her man's actions. What made Savage work in the 80s was the very dangerous game that he was playing with Elizabeth of being on the verge of outright physical abuse -- you just WANTED to see this guy get his ass kicked, not because he was the IC Champion, not because he came out to Pomp and Circumstance and spun around the ring like he was the best, but because he couldn't even be nice to his manager. You wanted Savage's ass kicked for Elizabeth's sake.