Anyone able to help point me to server software I can use to run my own GameSpy Master Server similar to QTracker so I can play some of the GameSpy enabled games with friends with out having to rely on another central server that might go down? (I assume QTracker won't be any more reliable than GameSpy in the end...)

Here, catch! Its hot!

Thanks for the attempt but that's the answer everyone has... however they expect you to point to their master server which is what caused the problem in the first place... only it was the gamespy master servers. I assume qtracker will be even less reliable because they don't seem to have a very big network to depend on.
I did find software which I can use kinda... 333network's master server server. Has a windows port & seems fairly popular in the unreal tournament crowd. Sadly the source code is missing a source file (gskeys.c) which the few people in their irc channel were unable to help with. :-( So no compiling for me. Sigh.
I might try an older project which is barely breathing I take it but since I can't program I have no hopes it'll actually compile for windows. Called OpenSpy.

If you are straight windows guy, do not forget that you can run any non-proprietary system unencumbered in a small VM and then share them visible outside your host network. It does not really have to be windows only, even if your host os is windows.

I don't know the subject, thus posted what I could. You might also try to post in a specific game forum (UT) right here.