You only need to include the non-standard textures.
When i build a map i mostly create a new folder that holds all the new textures. The same for shader-files.
so sth. like this textures\mynewmap\
and scripts\mynewmap.shader
(note: the folder-name and the shader name don't need to be the same)
So to make my pk3 i basically just need to add the new texture folder and the shader file to be sure that all textures will show up.
Another way is the q3map2toolz-pk3Maker
(
http://hro.planetquake.gamespy.com/webs/q3map2toolz.htm)
However it's designed for q3, so all standard-nexuiz textures will be added to your pk3 and _bump nad _gloss textures won't.... But maybe there's an option to add these. Haven't tried it lately.
I also use q3map2toolz for compiling. check it out.
bleach->aneurysm->straledm5->dieselpower->space-fun->o-fun->runningman->runningman1on1->aggressor(conversion)->soylent->bloodprison->bluesky->ruiner->reslimed->strength