At perl.org, we use Nodeworks to do our link checking. I dealt with the monthly reports today, and was happy to have a concise, easy to read list of all the dead links. There's a whole bunch less now.
This is all part of my evil plan to keep perl.org in shape. Last week I went on a 404 kick.. and I'll be doing it again soon, since more have had time to gather in the logs.