I didn't see anything around specifically on this, but it is fairly simple to get MOO1 and MOO2 running natively in linux.
- I'm running Ubuntu 9.10 and installed WINE and dosbox from the repos.
- Then simply download the installer, right click and launch with WINE (it is one of the right click options usually).
- The game will install.
- Then, browse to /home/{you}/.wine/drive_c/Program Files/GOG.com/Master of Orion 1 and 2/ and you will find MOO1 and MOO2 folders. You can copy these elsewhere, or run them from here through dosbox in Ubuntu.
And that's it. I've only played MOO1 heavily, and it ran great. MOO2 also ran, but I haven't actually played it yet, so not sure if there will be any late game problems.
Might be nice to have a plain old .zip package for us Linux users. ;)
Also, I've never played MOO before, but coming from a long Civilization background this is one of the comparison games you always hear about. And I must say, it is similar, but with its own twist. A fantastic game if you like these types of games.
Thanks GOG for the opportunity to try it, and shame on you GOG for giving me the opportunity to try it. What a time sink this is going to be. :p

Hear hear!
I run Ubuntu on my netbook and enjoy several of GOG's DOS offerings flawlessly.
A bit more information can be had here:
http://ubuntuliving.blogspot.com/2009/06/playing-dos-games-from-gog.html
Of course you might get less work done on your 'serious' Linux computer.

Another linux user that loves GOG here!
For my setup, I use innounp to extract the files directly from the installer. (My distro, Arch Linux, has a pkgbuild script for it in the user repository)
Then I edit the dosbox.conf file a bit and set up a nice soundfont in fluidsynth.
As for GOG distributing a zip? C'mon, the linux way is a .tar.gz! (Same DEFLATE compression algorithm though, heh heh)
A .tar.xz would be even better!