My personal two cents.
I feel that the Joker wearing make-up is going to be a very important part of the character. Let's assume for a moment the joker begins as normal (if slightly unhinged). He starts to get crazier, and gains (through whatever means) the Cheshire Grin. Now, we can reasonably safely assume that he gains the Grin through someone else's actions, starting his downward spiral into psycho-hood. Now, by putting on the make-up, he acknoledges and accepts (hell, he even praises) his own insanity. In the clasic origin, where he falls into a vat of chemicals, there is one thing missing - choice. With the make-u, he becomes an avatar of chaos and insanity, a symbol, in the same way that Batman chooses to become a symbol of law and order by donning the Bat suit (I feel that there's going to be a very storng theme of law and order in this movie - even his costume resembles actual knightly armour now,r ather than being 'scary'; not that it isn't intimidating).
Of course, this is just my thought, and your miles may vary, but that's what I do in Nolan's shoes