Well, I'll start with saying I loved both films. I did not expect to enjoy Iron Man as much as I did, and I was impressed with Ledger's performance in the Dark Knight. Overall however, I believe The Dark Knight is a superior film. This is my reasoning, and I'll start by saying it has to do with Ledger, but I'll also say that Ledger is not the entire reason I love the Dark Knight better.
It is typical of many superhero films to have very very high stakes such as, 'well the world's going to end if you don't beat this guy.' This new Batman series I feel is able to still be very dramatic, but at the same time, the world doesn't end just because The Joker 'wins.' The Joker is a terrorist in this film; his only goal is to ignite chaos and doubt into Gotham and completely demoralize it. The world doesn't end if Gotham becomes a hellhole; it becomes a tragedy, not an apocolypse.
Iron Man follows the same, predictable, power-crazy villain that could take over the world. Granted, Downey Jr. does a fantastic job of portraying a flawed hero, as is the tradition of Marvel, but the story of the film as a whole is nothing new or even interesting. Of course to make up for this fact, we're hit with cutting edge special effects and 'explosions,' but I think where Iron Man falls short, The Dark Knight blows it out of the water.
One of my favorite scenes in the Dark Knight film is when Batman and the Joker are in the interrogation room. We really got a glimpse into the mind of this madman, and how he acts almost biblical; acting as the devil, tempting a believer. It was brilliant, because you don't see it in other super hero movies.