I've always been partial to "Hyperspace," from John Williams' magisterial score for Empire Strikes Back. It does a great job of blending all the various character themes from the movie. In a lot of ways, it's an earlier, better version of "Duel of the Fates," minus the now-horribly-cliched vocals.
I should add, though, that Howard Shore's "Breaking of the Fellowship" can make me ugly-cry like Claire Danes. (Not so much the Enya part.)
Though this might be my favorite of all:
I always figured Shore listened to a lot of Morricone.