For anyone who needs a free web based Bug Tracking system programmed using PHP/MySQL, check out Flyspray.

I searched very far to find a web based program to track the bugs in the website I work on in ASP/MS-SQL. I know PHP/MySQL so I was able to setup this bug tracker, and fortunately I can modify it to do things I need it to do.

Its features appear to be good enough for tracking bugs in actual software, and it can be setup to suit those debugging web based software.