Still havan't seen "Charlie or the chocolate factory" (nor the corpse bride). 
But as far as I am concerned I only thought "Planet of the apes" to be a failure. Liked "Big Fish" very much, (though I prefer "sleepy Hollow" )
Pee Wee has also aged well in my memory. I'd like to see it again. 
The only others I have partially problems with are "beetlejuice" and "Mars Attacks!".
Talking about Burton, I should really rewatch most of his films.
But I like it most, when he is "darker" (my favorite is "Batman Returns"). In fact I think he hasn't yet been dark and quirky enough. Imo there's still a lot of hidden potential in him.

Ah, I think I'll start a rate the director thread on him right now. Would be interesting to see your preferences listed