This is the folder structure:

./crosshairs/          Crosshairs
./env/                 Skyboxes
./gfx/                 Console backgrounds
./lits/                Colored lighting files (i.e. ".lit" files)
./maps/                Custom maps
./progs/               Models
./skins/               Player skins
./sound/               Sounds
./textures/            Map textures
./textures/bmodels/    Healthbox and ammobox textures
./textures/charsets/   Console characters
./textures/levelshots/ Level screenshots (loading screen while loading a map)
./textures/models/     Model textures (e.g. weapons, armors, projectiles)
./textures/wad/        HUD textures (e.g. armor icons, health icons, big numbers)

If a folder doesn't exist, simply create it.

You can open .pk3 files with any program that opens .zip files, and .pak files with "pak explorer". You can add or remove files, with caution.