Powdork - 6:01 am on Oct 12, 2005 (gmt 0)
Would something as simple as xenu work on your php/mysql site? The chances are greatest that this is a result of some sort of manipulation of external links (intentional or otherwise). Set the spider to pull out all external links and then you examine them on a page by page basis. Maybe you have an employee hiding some links to a site he/she is working on.