I found several errors with this game, playing on Mac (10.7)
-Change of options in-game are not saved: control binds, campaign update, tech room... all these things disappear when I restart the game. Additionally, the "Alt"-bind refers to "Cmd"-key on Mac, making the game unplayable with "Alt"-binds (Cmd-H minimizes window, and it's not possible to properly return to the game after that)
-Some missions could not be finished succesfully. E.g.
"paving the way"
"The Darkness and the Light"
"Failure to communicate"

in these missions, the scripted events do not take place properly, even though I fulfilled all directives. Ships sometimes do not leave the sector, so that I cannot jump out. Sometimes it helped to reinstall the game, but not always. Aside from this very good port, this is annoying! Anybody else have these problems?

EFDM

The scripted events problem I think is with the game not the port - I'm pretty sure I've see people complain about them in Windows too, sometimes solving them, sometimes not.

e.g.
http://www.gog.com/forum/freespace_series/paving_the_way_the_ship_just_sits_on_the_jump_point

I use FSport to play the game - it ports FS1 into the Freespace Open Engine and makes things really nice to play. Freespace Open makes FS2 a native Mac application, upgrades the graphics/AI/etc, and fixes a lot of issues. It also has a bunch of mods available for it, one of which is FSport which lets you play FS1. You can even play it without high-end graphics by not using the high-res assets if you want the old-school feel, but the upgraded graphics are gorgeous.

You should check it out as an alternative to playing the GOG-Wine port.

http://www.hard-light.net/wiki/index.php/Getting_started

Mac install instructions

I had some problems with the FS1 cutscenes so I ended up replacing the the .ogg movies from FSport with the original files. Other than that it should be fairly straightforward!

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However, to help you with the GOG-wine port, for your "cmd"-key problem, go to FS1, right-click and say "show package contents", then open Contents>Resources and right click Freespace (again) and say "show package contents" (again). Then open "Wineskin", hit the Advanced button, then the Options tab. Click "Option key works as alt". Eh viola! :)

Now that your settings aren't being saved is odd ... I'll have to get back to you on that since I use FSport to play FS1 not the Wineskin port so I've not really played around with it.