There's been discussion since Beta about how much people would like Star Trek music in-game. And I know Cryptic has personally met with the music rights holders to try to negotiate a price but that it's been out of their budget so far.
Still... I don't think the music used has to be the main series titles, necessarily, to generate the emotional resonance needed. And I think those songs, being the work of big name composers, is probably behind a lot of the expense. However, it seemed rare for you to hear the main titles actually used in a show.
I'd like the suite from "The Visitor" to be used at Deep Space Nine. I think it would do a nice job thematically echoing how the place was brought to prominence by Sisko and how his absence casts a certain glow about the station while also evoking the idea that he still watches over it.
I'd also like the flute theme from "The Inner Light" or its orchestral arrangements to be used on non-combat missions like "Scan 5 Anomalies", "Aid the Planet" and diplomatic missions to underscore the feeling of peace and exploration we should feel.
The TOS fight music was composed by Gerald Fried, who isn't necessarily the name that a Horner or a Goldsmith or a Courage is. I think that would be great for dueling.
Beyond that, there are some themes associated with Trek that don't fall under GNP Crescendo's (apparently expensive) rights arrangements:
- Music from Prokofiev's Romeo and Juliet, used in STIII for the theft of the Enterprise (Very epic sounding and great for Klingons and very oppressive visuals such as fighting armies or infiltrating buildings)
- Goodnight Sweetheart, by Ray Noble (Used in City on the Edge of Forever... Good for sentimental/romantic storylines. For example, beaming into a village where someone pleads with you to save their family. If you really want to impress the player with how modest and happy a village is, great choice. May be worth a few arrangements in different styles, tailored to the setting, as it's a bit heavy.) http://www.youtube.com/watch?v=T_Y1hcHnUrg