In my oppinion, Silent hunter II had the most fitting music. The march elements and the consistent background beat was perfect for a submarine simulation.
I must say that aside from Wing Commander (all of which I feel had good music, and I loved how it changes with the scenarios) I like the music for Deus Ex, and how it changed to match the area that you were in.
I have to vote for the Rainbow Six Series.... Bill Brown is absolutely the top video games music composer. As much as I like WC I honestly have never enjoyed the music. Rainbow has these little strands of music which come up ingame when You're doing something stressing and it so adds to the experience. That in my mind is fitting music, when it's not the same thing with the music off.
I liked how it followed the mission situation, the tunes would change according to what was happening. That was original at the time, and I never got tired of the music.
I would have to go with Wing Commander IV. The use of full orchestra music really set the mood. Prophecy was good music, but it just didn't seem to catch the mood that WCIV did.