Now, I've looked through this thread, and noticed that Shirley Walker's theme for B:TAS's continuity has not been mentioned.
That is my favorite Batman theme, at least, for me.
Though I love Danny Elfman's Batman 89 score, I feel that it is a little dated, and too stylized to work in Nolan's film. The notion that they should build up to Elfman's theme in this new continuity is absurd for many reasons: legal dealings, re-tooling of the already established music, and finding a way to accommodate for the theme in the films or the other way around, to name a few.
Zimmer and Howard's collaboration worked for the style, tone, and pacing of Batman Begins. Even if Howard is not teamed up with Zimmer for TDK, I'm fully confident that Zimmer will deliver and meet, if not exceed, expectations. Look at his PotC:AWE score, and there is proof that when he is devoted to the film's score, he can do very well.
Also, as a side note, there is a "COMPLETE PROMO SCORE" for Batman Begins floating around the internet. It is the real deal, as it has excellent quality end credits, unreleased music, some alternate cues, etc. Its worth a search.