Sorry for the lack of updates recently, I am still in the process of handing off my Bootstrapper 'stuff' to the new owner, David Guyer. David's a great guy and you can see him trolling around the MSDN forums for ClickOnce and deployment projects at:
The big news however, is that I have finally uploaded the first edition of the Visual Studio 2005 Generic Bootstrapper SDK! In it you will find some tools, files, and documentation to help you in creating custom packages.
Unfortunately with the team change I haven't been able to make it is as grand as I once envisioned, but it should definitely be a good resource to anyone new to creating custom Bootstrapper packages. If you have any feedback or requests for additions to the next Bootstrapper SDK release please use that contact link and let me know!
The SDK is distributed under a Shared Source license so if it manages to make your computer asplode (which it won't) please don't sue me or Microsoft.