What I've always done is go into Radiant after packing your .pk3 and using the
Find and Replace feature in the texture browser to make sure the map is getting the textures from the .pk3 rather than your .../base/textures/... folder. There might be a more efficient way of doing it. In fact, there likely is. Using Find and Replace, though, is fool proof, if not a bit lengthy.
edit: You might want to make the topic title a bit more
on-topic. I thought you were going to be asking about how to release a texture pack, or where to find one, or if there was a popular one available. Try something along the lines of "packing textures into a .pk3", or "textures in a .pk3?".

Hope I understood your question.