I often get asked about best practice for deploying and migrating BTS applications. In 2004 I used Scott Colestocks Deployment Framework for BizTalk which worked well. In 2006, there is a bit more build in flexibility and support for variables with MSI installer cababilities. See the Selective Binding Import SDK example.
For more deployment best practice advice see:
“Deploying and Managing BizTalk Applications“
“Best Practices for Deploying a BizTalk Application”:
http://msdn.microsoft.com/library/default.asp?url=/library/en-us/BTS06CoreDocs/html/97ebf479-0dc5-4e95-b409-d3b6ad3d60d0.asp