I'm trying to run FS2 on Linux Mint under Wine, and it's working great but for the fact that half the screen is not being displayed (see screenshot.) I don't expect, or need, linux-specific help, I just need to know how to either change the resolution or make the game run in an window, preferably from outside the game.
I can't run the launcher, FRED2.exe and Freespace2.exe both give me the "cannot be run from a drive root directory!" error. The game is installed to the default folder, drive_c/Program Files/GOG.com/Freespace 2, so I don't know what's causing that. If I can fix the display problem without fixing this error that's fine, I don't need FRED or the launcher really.
I do not get the display error during the intro cinematic, just from the login screen on, including during actual gameplay.

Glad you got it working!

I've got a problem with Freespace 2 displaying as well. I'm running Windows 7 and when I launch FS2, the screen flickers like mine usually does when starting a full screen game, and then it goes back to my desktop and I can't open the game window. Any ideas what's wrong?

I'm afraid I can't help you too much with Freespace 2 vanilla ... have you tried downloading and installing Freespace 2 open? There are threads here on how to do it and contains a lot of improvements to the game engine - especially in the purty graphics department. It also helps with compatibility to newer and different OSes.