Assuming that you have your links in the database when you parse them out just add a link to a broken link script and pass the unique id. That script can update a flag on the record as "broken". Then when you next show the page you only select the records which haven't been reported broken.
As an admin you can then select all the broken links and either delete or update.
count links out...
I use a script I call links.php on several sites. When I display a link it actually calls links.php which finds the real url and redirects. Before redirecting my stats counters get updated.