Pakrat is a GUI replacement for Valve's Bspzip application.
Pakrat has the ability to scan a .BSP file for all texture, material, and model files used in the map and automatically embed custom content into the .BSP file.
Pakrat is known to corrupt files in the .bsp file if you delete and re-save packed content. For Pakrat to correctly pack your custom items, you must make sure to add everything to the .BSP file without missing anything before you save the .BSP again. Also, overwriting an existing version (For example overwriting your currently opened map in Pakrat) will also corrupt your files.
Pakrat is known to corrupt navigation fiels as well, so include those seperatly.
Use at your own risk.