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”: