I don't like the statement that you're looking at using a lot of BOE's. They can be good for a climax if you do them properly, but their number should be kept very low in any campaign.
Oh, and by killing Deuteronomy, you're killing perhaps the best track in the entire game. It's the prototypical music of shivan encounters, and that wailing horn really is Freespace music more than any one trend.
EDIT:
Originally posted by Andreas
Arr, I forgot the Monolith as well, bloody great track there.
But it was used at least twice in FS1 main campaign (I think at least in Failure to Communicate and of course, the last mission).
For the record, the only mission to ship with FS1 that used that track was m-duel.fsm, the multi mission titled "Leviathan Duel". My guess is that the track was intended for the last mission, but the designers liked the ambience of no music better for the situation in the end. Powerful track, and a real shame it wasn't acually used in any missions. Silent threat uses it in a couple more places (maybe even one in the main campaign) but it's still relatively rare.
And for whoever said that FS1 tracks are lower quality must be on something. Their sample rate is lower and they are only mono, but the quality is top-notch. They are better-composed than the FS2 tracks, and the bit of scratchyness that is introduced just adds to the immersion IMHO.