This one's going to be rather unothodox, but....
http://www.amazon.com/Godzilla-50th-Annive...0757&sr=1-3Akira Ifukube's GOJIRA. The soundtrack to the film of the same name (which was later recut and released in the States as GODZILLA, KING OF THE MONSTERS). The American version didn't keep the music intact for nothing: it's, dare I say, one of the best film soundtracks out there, and certainly dark enough for you.
In fact, I'd reccomend pretty much any of Ifukube's compositions, film soundtrack or not. He wasn't considered a national treasure to the Japanese for nothing...
In the same vein, Koh Ootani's GODZILLA, MOTHRA, KING GHIDORAH: GIANT MONSTER ALL-OUT ATTACK is rather nice as well. More traditional classical blended with some synth elements. Not bad, though somewhat repetitive.
Honestly, that's one thing that the Godzilla films have always had going for them: aside from a few exceptions, the music has been excellent throughout the entire series.
EDIT: oh wow, didn't realize how old this thread is...