Always remember that you must trust the writers of the CGI script/programs or your ability to spot potential security holes in CGI, whether they were deliberate or accidental.
All the CGI scripts will run as the same user, so they have the potential to conflict (accidentally or deliberately) with other scripts. For example, User A hates User B, so she writes a script to trash User B’s CGI database. One program that can be used to allow scripts to run as different users is suEXEC, which is included with Apache as of 1.2 and is called from special hooks in the Apache server code. Another popular way of doing this is with CGIWrap.