I previously wrote an article about a tool that could help you undeploy BizTalk assemblies with its references, without going through the pain of keeping track of all assembly references.
The tool has now been updated for better support of dependency tracking along with some other minor UI changes.
The application requires .Net 3.5, which, if you haven't got it installed, can be found here. If you choose not to run the application on the server, make sure the assemblies you're about to uninstall are deployed to the computer from which you're running the application. This is because the application needs to access the assemblies to get its dependencies.
Download
HTH