I don't know any of them .. i'm doing PK3s by myself.

this is a good idea for making an tool like this if there isn't one already done.
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epsislow

Yeah,
I never find "good" solution also, i try many programs, but no one are good. Just do it by yourself!
Pk3 are simple Zip archive, open it with winrar or winzip.
but you already know that i think
I've also this problem, it takes so much time to seek textures, put'in the pk3 blablabla, the only way i find is, taking a pure q3 without any unofficial pk3's, create one pk3 with simply maps folder, and put my bsp in it, then start playing, no texture on map, i open console, i take a screen, then back to windows, i add every textures 1 by 1..... hard long work