I created this tool ages ago and have been using it on projects for a while. Ive eventually got around to cleaning it up and doing some documentation for it so I have now made it available on CodePlex.
Basically the tool allows you to generate an MsBuild script which will let you do all of the build and deployment actions to compile and deploy your BizTalk solution.
It also produces a script which is well structured and easy to extend.
If you want to know more check out: http://www.codeplex.com/BizTalkMsBuildTool