I had an issue with Netbeans 6.8 where the auto-complete for PHP functions stopped working. It would work with functions and methods defined in my project but wouldn’t auto-complete any native PHP functions.

The fix for this is to delete the var/cache/index folder contents  in the users Netbeans directory (in my case, ~/.netbeans/var/cache/index/ ). Close and re-start Netbeans for it to take effect.