create a field in the user table called verified.
send an email to end user with a link to a php file on your webserver, using a random string. Put this random string in your user table.. call it.. verifystring.. or something.
then in the php file.. when the link is called..
you do a search with the variables..
the userid, username, emailaddress and verifystring.
if all match..
then mark the verified field with a 1.