Well, it sounds like you have some kind of user authentication in place, so everybody should have a unique username, correcto? If so, then use their username as the naming convention for their files.

username-originalfilename.pdf

If you want to go a step further and see if that particular user has already uploaded a file of the same name and type, use file_exists() and decide at that point if you want to overwrite the file or append something additional to the name.
-m