> 
> Except that users who run scripts that allow them to upload files are owned by the web server user and thus don't get counted towards their quota.  With cgi you can get around this using suexec, but not with php running as a module. (watch out for photo album programs).
> 

Give each user an individual group, and make the group of his or her home
directory that particular group.  Any file created in the home directory
will be in the user's group, regardless of who owns them.  Then a quota
on the user's group will put all files in the user's home directory under
quota.

David S.