I just spent a lot of today customising Bugzilla even more.
All reports and queries now have a general theme that provides a lot more consistancy, there are 3 extra reports that save messing around with the advanced query interface, and customising fields and drop downs is complete.
Essentially I have hacked a small amount of templates and code to mould bugzilla to our needs.
For my next trick I will integrate some CVS reporting into it.