TDK is a follow-up to a hit movie, where IM is just starting off.
The better comparison would be "Batman Begins" to "Iron Man", but even then... Batman had been attempted 5 times before and kinda had a head start on fine tuning.

Prep time, if you will.

As fara as box office, TDK will murder everything this Summer.
As far as fresh out the box stories, I say Iron Man takes it.
As far as a fun movie to watch, Iron Man takes it.
As far as gritty drama, TDK wins.
As far as performances go, Ledger's Joker takes it.
Not taking away from Downey, but we haven't even scratched the surface of the Tony Stark character.

And frankly, it'd be quite foolish to think that any follow-up to Iron Man would be able to compete on TDK's level.
I don't think Marvel would even take it that dark with Stark and 'nem.