Some people requested a feature to have a .cfg file that gets automatically executed when Nexuiz is started while a pk3 is installed.
I have to tell you - that feature was there all the way, and can be enabled by config file hackery.
http://mensa.ath.cx/~polzer/temp/divVerent-1.pk3
http://mensa.ath.cx/~polzer/temp/divVerent-2.pk3
If you install just one of these, you'll see a "Hello, world 1" or "Hello, world 2" text on startup in big letters.
However, if you install both, you can see both texts - and they don't "override" each other!
To generate such pk3s, you need this tool:
http://mensa.ath.cx/~polzer/nexuiz/nexoexec.zip
and read the included documentation.
Although I can't stop you from modifying the tool, do not do that, as it will severely break the compatibility between pk3s created by this tool.