Cross-platform: wxLauncher 0.12.x Test Build (http://www.hard-light.net/forums/index.php?topic=89162) (ongoing project for a unified launcher, you should upgrade to the latest RC/test build if you have not yet)
Important: For best compatibility with FSO 3.8 and later you should use at least wxLauncher 0.12.
Windows: Launcher 5.5g (http://scp.fsmods.net/files/Launcher55g.zip) (Mirror (http://scp.indiegames.us/builds/Launcher55g.zip)) (Mirror (http://www.mediafire.com/?wdvzn7hhhzh418m)) Not compatible with Windows 8+, use wxLauncher above
OS X: Soulstorm's OS X Launcher 3.0 (http://www.hard-light.net/forums/index.php/topic,51391.0.html)
Linux: YAL (http://www.hard-light.net/forums/index.php/topic,53206.0.html) or by hand (http://www.hard-light.net/wiki/index.php/Fs2_open_on_Linux/Graphics_Settings) or whatever you can figure out.