Secure system calls -- how

Hi list, I'm doing an intranet website for managing users. I need to be able to change passwords, move files and folders around and that kind of thing. What is the best way? Obviously I can't run the webserver as root. In an earlier version I wrote update information to a table and had a cronjob scan that. But that solution is no longer good enough -- I need to call system functions directly. I can't find any thorough articles on this subject, but surely someone here has some ideas or some pointers. Thanks, Niels