The TOS theme works in the context of the show, I think, but seems a bit cheesy on it's own, though I imagine a new arrangement could be quite interesting.
The TNG theme is great, but it loses points for also being the TMP theme.
DS9's theme, to be honest, never quite did it for me. If I had one sticking point on that show, it would be that the music of that series was mostly Berman's choice of sonic wallpaper, and the theme doesn't fair much better, in my opinion.
VOY's theme, as others have echoed, is spot on, perfectly capturing what the mood was (or should have been) on that series.
ENT's theme gets dumped on, but I don't think it's too bad, at least in the first version, from seasons 1-2. It captured the spirit of the show, and worked well in conjunction with the great looking title sequence. When they upped the tempo, however, it was all wrong, both musically and stylistically with where the series was at that point. Even though, as I said, the DS9 theme doesn't do much for me, the change in tempo in season four was the right thing for that series at that point. ENT in season three feels like it's trying to emulate that change, but in all the wrong ways. Oh well.
Voyager wins.