There are several 'themes' in the BB score. They are just not linked to any of the characters, more to psychological happenings in the story. An attempt to clarify:
Piano themes:
Theme 1: the beginning of Corynorhinus, Macrotus (0:39). In the expanded score of BB, the track is called "Gotham". It also appears in the end credits. For fellow musicians: you can find the sheet music here:
http://www.gamingforce.org/forums/attachment.php?attachmentid=18510&d=1176500145
Theme 2: appears in Eptesicus. A simple three note motif: A - E - B - E - A - E - B - E, etc.
Strings:
Theme 1: Macrotus (1:09), Corynorhinus (1:57).
Theme 2: the staccatto strings (with brass) can be heard in Vespertillio, the second half of Eptesicus and throughout Molossus. And in Jablonsky's score for Transformers.

t:
Theme 3: Molossus (3:33) I'm not sure if this is a seperate theme, but I think this is the theme that Zimmer wants to use in TDK. I'm not sure, but I believe it wasn't used in BB. It starts with a synth bassline. Then the brass, percussion and strings come in.
Percussion:
The beginning of BB. And the track Vespertillio (Travelling The World on the expanded score).
Then there's some separate stuff like the end of Barbastella (the scene in the cave with the bats) and the action music in Myotis (Bruce Wayne escaping from the League of Shadows).