Whilst it seems to only be on the soundtrack to Batman Begins, not in the actual movie (at least, not in its entirety), "Lasiurus" possibly sums up the essential character at the heart of Batman better than any piece of music (even some of the other fine pieces listed here) ever will — it's dark, brooding and melancholy, and yet there's a subtle note of hope weaved in there that gradually and powerfully builds to a crescendo, giving the listener the impression that the night will end and evil will be overcome...
Molossus, which also fits Batman flawlessly - it's nothing but 4 minutes of pure badassery, with an always-present sense of heroism and determination that reflects the fact that Batman will never, ever give up until all of Gotham is safe from crime.
The opening track "Why So Serious?" sets the mood for the entire film. Amazing how much horror is contained in a single note... Listen to it over headphones, or surround sound in an acoustically perfect room; that single note jumps around, well... chaotically. The Crystal Method's Remix of said song is not quite as creepy, yet... it is. In its own "Crystal Method way."
The last minute of Aggressive Expansion. If "Why So Serious?" builds up the tone of the Joker, this song smashes it down on you like a 5000-pound hammer. It's impossible to listen to this song without imagining him bursting into the room and holding a knife to someone's neck at the last second, and to top it all off, the scene it's used in is when he kills the goddamned judge and commissioner.
I'm Not a Hero. Particularly the subtle similarity to the Elfman theme around the 4 minute mark.
Harvey Two Face, especially in its stirring reprise of the love theme. Awesome in spite of the fact that the ending part doesn't show up in the film.
The original release of the soundtrack ends with the 16-minute long suite A Dark Knight. Emblematic of the competing ideals between Batman, Joker and the people of Gotham, the notes come after the other in a tapestry of epic conflict—with the last notes devoted to the overwhelming crescendo of Batman's saga-wide Leitmotif, yet still undercut by Joker's own unsettling electronic note, the very same one from "Why So Serious".
The re-release, in turn, grants us the "A Watchful Guardian", the very same music playing in the closing minutes of the film—Batman taking the fall for Dent/Two-Face's murders, the Gotham Police chasing, and Gordon's closing monologue. Notably, the last notes also close with Joker's electronic note, but at the very last second, is overwhelmed by the "flapping wings" leitmotif of Batman.
The Bane Chant is a masculine theme that fits Bane, one of two main antagonists of the movie.
"A Fire Will Rise", the third trailer theme, which is mind-blowingly epic and tragic, fitting perfectly the mood for the finale of the trilogy.
While this isn't connected to the movie directly, Hans Zimmer created a hauntingly beautiful track called "Aurora" honoring the victims of the Aurora Theater Shooting. The Dark Knight would be proud.
"Gotham's Reckoning" plays as Bane and his henchmen kidnap a nuclear physicist and wreck a CIA jet in mid-flight. And now the complete score has been released, witness the incredible drums at the end of the film version of that track.
All Out War (imagery contains spoilers) plays during the final battle between Batman and Bane. It starts with Bane's Leitmotif, but then, 30 seconds in, it turns into something entirely different, becoming both intense and extremely climactic, and it really does hit home that this is the Last Stand for both Batman and Bane. That whoever wins gets to decide Gotham's ultimate fate. That this is truly the Grand Finale. This theme screams "It. Ends. Here."