I still like my "sanity deteriorating/skin deteriorating" theory.
Like, he fell in chemicals sometime during the time at the end of Begins. Batman might have been the "cuase" of it. And Batman just knows him so far as a faceless thug trying to hijack a chemical plant's payroll. Okay, skip ahead to TDK, where Joker's natural skin and hair colors begin to wear away. And, since he seems like a very vein person, so does his sanity. Which coincides with a Miranda Fox report that says Joker will grow more and more Jokerish over the course of the movie.Now, his skin and hair colors begin to wear away, as evidenced by the picture of Heath sans white skin and scars, at the bank, with that little tuft of green hair. That's the first sign. Blah, blah, blah it deteriorates more and more all over his body, blotches of white and skin tone. Giving the ILLUSION of a man painting his face white. You don't see the rest of his body, of course, so it DOES look like a normal man painting his face white. But since he laughs and smiles so much, the wrinkles wear the skin pigment away faster. That's also true, that when you smile and laugh at extremes all the time, your face does stretch and form slight or major wrinkles. So the pink skin would deteriorate faster. Okay, now Joker's pretty much teetoring(sp?) on the very brink of falling into the abyss. Cut to Batman SOMEHOW inadvertantly cuasing Joker's scar(only one side, it'd be impossible to scar both sides at the same time). That basically sends Joker completely over the edge, and simultaneously cementing his hatred and obsession with Batman. Also, he carves the other side of his face up, just to match it. Becuase, one side is very badly cut, like from a freak accident. But the other side is very cleanly cut, like it was done on purpose. And, over the course of the movie, he puts on either flesh-colored or white make-up, depending on the situation and the need at hand. Maybe he needs to blend in, and puts flesh colored make-up over the white blotchy parts on his face. Maybe he needs to contribute more to the illusion and add a little white to even it out. Master of Disguise, of course. Add to the fact that Joker did apply flesh-colored make-up to bleached skin in his first appearence. Why not take it a step in another direction, make it more real, and make it to where he just needs to even it out a little. Becuase I doubt chemicals, even chemicals that WERE capable of bleaching skin and greening hair, would do it at one time. Since skin ages and hair falls out and grows back, it would be over the course of a very long time.
That's my theory. At least all of what I can think of right now. If I had more time, I'd probably be able to flesh it out a bit more.