I worked in a startup for several years where we started with GNATS, an open source tool, and essentially built our own elaborate bug tracking system on top of it. The argument was that we would avoid spending a lot of money on a commercial system, and we would get a bug tracking system exactly fitted to our needs.
Of course, it turned out to be much harder than expected and was a big distraction for the developers - who also had to maintain the bug tracking system in addition to our code. This was one of the contributing factors to the demise of our company.
