This Waits/Ledger thing has gotten blown out of proportion.
Whether he was inspired/influenced by Waits or not, Ledger still made one hell of a Joker. There were actual influences that they commented on, like Alex from a Clockwork Orange, Johnny Rotten, Pete Doherty but you know what? He transcended all of those. I don't see the influences, I just see the Joker.
The original vision was this weird, punk rocker, anarchist.
I think Ledger took all those ideas and instead made his own thing by taking it to a different place. I never saw Tom Waits eat shrimp cocktail. I never saw Tom Waits reading from scripted notes as he tries to pitch his little morality game to the ferry boats. I never saw Tom Waits dressed in Nurse drag cleaning his hands with hand sanitizer. Ledger's Joker is special and it isn't because of some awkward 1970s interview.