So the mod topic lately has been... not fairing so well on it's front page with some dead links and whatnot. I'm just mentioning the really important mods here because I love you all. Use the installer linked in here to fix the registry, which is exactly why UT99 won't recognize UMOD files. All you need to do is follow the links, click on the registry fix and it's download button:

http://wiki.beyondunreal.com/UT99_Registry_Fix

Also, check out this topic to fix the registry problems manually!

It really saved my bacon and it should do the same for you. Here are the items the GOG version has missing from the original GOTY Edition (as far as I'm aware) in UMOD format.

Bonus Pack #4 in UMOD format can be found here (Note that the GOG version has 1-3): http://www.fileplanet.com/53827/50000/fileinfo/Unreal-Tournament-Bonus-Pack-
ChaosUT: http://www.moddb.com/mods/chaosut
Rocket Arena: http://www.moddb.com/mods/rocket-arenaut

These renderers are a godsend for newer computers.

Updated OpenGL and Direct3D 9: http://www.cwdohnal.com/utglr/
Direct3D 10: http://kentie.net/article/d3d10drv/

And here are some really great looking Hi-Res textures for those that can run them: http://www.uttexture.com/UT/UT.htm

...Did I get everything absolutely essential outside of favorite mods?