Actually, I think one of my favorites might be the
Idol Theme. (It's only played just before Indy takes the Idol and then briefly in the
Map Room)
Other than that, I'd have to go with the
Ark Theme because it truely gives the Ark the mysterious character it has in the film.
In the end though, my vote goes with
The Desert Chase because I'd have to agree with
IndySeven that it really captures the spirit of the movie. It's also a genius 8 min piece of music on it's own, notice that there is little or no dialogue: the music tells the story. And what a story!