I don't know if this has been brought up yet, but anyway.
On the mission "The Great Preservers" (the first mission flying in a Vishnan craft) it keeps freezing. Basically, I'll click the "Commit" button, the mission will play for a second and everything will freeze. (Besides the music which keeps playing until I close Freespace 2 in Windows Task Manager). Just in case, I am using 3.6.10, and not one of the nightly builds. (I also tested one of them, same crash problem).
I'll also say that when i start it up, I get a message saying that something called a "flyby sound" is missing from the sound.tbl, perhaps related to the above problem? Even if it is related, it's caused no problems for me up to this point.
Otherwise the only other problem I had was the disappearing hud in the mission with the Kyton turning up after chasing the Duke. Could still fly, shoot everything besides gain missile lock really.