I have used StudetUniverse twice: for a one-way OAK-BOS in September and for a round trip BOS-SFO/OAK-BOS over winter break. No problem at all signing up and proving that I was a student (in fact no one ever checked, but I did supply a .edu e-mail address). Miles posted without automatically. (I even got the 500 mile bonus for using a self check-in kiosk in BOS). The fare for the round trip was something like $310 which was cheaper than what I could find elsewhere, though for spring break I found a fare on UA for $246 on ual.com, so no need for StudentUniverse this time. So I think it very much depends on the trip.

I would be more careful about international flights. Last year I flew LHR-MSP-LHR (via ORD) on AA on a student ticket bought from STA travel. Although I did not have to prove I am a student at check-in, the miles did not post because of the fare type.