Okay, here's what should work for you, if you don't understand something or have another problem with it feel free to ask.
1.) Install the Windows GOG UT2004 package with wine. I'd use a temporary directory, not the standard wine directory. I.e. a directory named tmp in your home directory (you have to create this first with mkdir), So the command will look something like this;
WINEPREFIX=~/tmp wine /path/to/GOGfiles/setup_ut2004.exe (WINEPREFIX is the environmental variable that tells wine which directory to use, the command above sets it to the mentioned tmp directory, but only for the wine command that comes after it)
Edit: It is a far better idea to use innoextract to get the files. See its man page for usage, it is pretty easy to use.
2.) Move the UT 2004 files to the folder you want the game to install to. I use the directory UT2004 in the home directory as an example.
mv ~/tmp/drive_c/Program\ Files/GOG.com/Unreal\ Tournament\ 2004/* ~/UT2004/ 3.) Get the Linux UT2004 Megapack from icculus (He ported UT 2004 to Linux for Epic. Remember his name, he was involved with most of the Linux ports of commercial games for the last 10 years or so. Nearly everything that isn't from id Software or Linux Game Publishing).
The URL to the Megapack is:
http://treefort.icculus.org/ut2004/ut2004megapack-linux.tar.bz2 Unzip that with tar to a temporary location:
tar -C ~/tmp -xf /path/to/Megapack/ut2004megapack-linux.tar.bz2 Now you have a directory called UT2004MegaPack move its contents to your UT2004 directory.
mv ~/tmp/UT2004MegaPack/* ~/UT2004/ I'm not entirely sure if the MegaPack is needed, but the latest patch says install it first. And there is other stuff than maps in it (i.e. updated binaries), so install it to be sure.
4.) Get the latest patch from icculus. The URL is
http://treefort.icculus.org/ut2004/ut2004-lnxpatch3369-2.tar.bz2 Unpack it to the temp. directory:
tar -C ~/tmp -xf /path/to/Patch/ut2004-lnxpatch3369-2.tar.bz2 Move files into your UT 2004 directory:
mv ~/tmp/UT2004-Patch/* ~/UT2004 5.) You'll need to get 2 libraries that the original Linux installer on the disc provided. I made 2 tarballs off them, for 32 and 64 bit respectively. You'll find them at [url=http://www.unix-ag.uni-kl.de/~deusser/UT2004]http://www.unix-ag.uni-kl.de/~deusser/UT2004[/url]/
For your 64 bit system get [url=http://www.unix-ag.uni-kl.de/~deusser/UT2004/ut2004-libs-amd64.tar.gz]http://www.unix-ag.uni-kl.de/~deusser/UT2004/ut2004-libs-amd64.tar.gz[/url] and unpack them into your UT2004 directory.
tar -C ~/UT2004 -xf /path/to/Libraries/ut2004-libs-amd64.tar.gz 6.) The last thing you'll need to run the game now is the CD Key. I think every GOG copy of UT 2004 has the same but it would be a bad idea to post it here. But you can get yours pretty easily from the registry of the wine directory where you installed the game.
So in this case you'll need to open the file ~/tmp/system.reg and search for CDKey. Copy the value of the key (which should be 4 groups of alphanumeric digits with 5 digits each, seperated by dashes).
Create a new file called cdkey with you text editor in your System directory of your UT2004 directory. So in this example it should be called ~/UT2004/System/cdkey.
Paste the CD Key into it and save.
7.) Test if the game runs.
cd ~/UT2004/System
./ut2004-bin-linux-amd64 or
./ut2004-bin on a 32 bit system.
The game should work now, but you'll want to configure the graphics and your player character for multiplayer. I tested multiplayer and single player and both worked flawless. The only problem I had was that I had now sound, but that was a problem with my OpenAL config (the sound system UT2004 uses but not many other programs I use regularly)
The only minor problem this method still has is that you need to start the game from the System directory so it can find the 2 libraries. But I'll look what the original installer did about this and post a way to have some convenient short cuts and start menu entries here, hopefully.
Edit: The easiest way to make a shortcut is probably to create a link to the ut2004-bin-linux-amd64 binary on your desktop or in the start menu of your window manager. Keep in mind that the UT2004/System directory needs to be set as the working directory. Here is a link to the icon file the original Linux installer provided so your desktop shortcut will look like it belongs to UT 2004: [url=http://www.unix-ag.uni-kl.de/~deusser/UT2004/ut2004.xpm]http://www.unix-ag.uni-kl.de/~deusser/UT2004/ut2004.xpm[/url]