we have tried to get it working using the windows compatibility tool to no affect!

"it complains about compatibility with the system"- You

That's pretty vague. I only use my XP boot for the Quake games, but I also run Vista Ultimate 64 on the same machine and it runs Q3 fine'ish. Used to have an issue with the textures, but I got that corrected somehow. And there's also the inherent mouse accel in Vista, AND the inability to overclock my USB port for my mouse..

But... technically, it should at least let you play.

... Why would you want to uninstall quake 3?

Copy the necessary files from your CD to the destination on the HD that you want.

Patch the game up to the necessary state and then run it.

In the end, start it up and try to connect and stuff and it WILL whine about missing CD key.
Enter the key and your fine.

I'm not sure if iÍ'm late but open the quake3 folder in the CD (you an see it in the picture) and there's another setup.exe and that exe worked just fine with my rig. And yes, I'm running vista 64bit.

who the fuck uses the installer anyway?
see that Quake3 folder? copy it you stupid bellend!

As someone else stated above me you just explore the cd and use the setup file in there. Installed it myself last night on vista x64.