When I run msbuild on my BizTalk 2009 .btproj file, the default targets execute and the project is built.
Is there a target I can invoke to deploy the project?
Unfortunately no, there is not.
However this would probably be useless because as soon as you got solutions that consist in multiple modular projects and solutions, there would not be an easy way to manage the dependencies between them.
Instead, you might be better off investing some time to setup a proper deployment infrastructure. As Thomas suggests, you shoud have a look at the extensive Deployment Framework for BizTalk on CodePlex that covers just about any requirements you might want to address with BizTalk.
If that seems too intimidating, I suggest you build a simple deployment framework using msbuild. It is actually quite simple and straightforward to do. building the individual projects would be a breeze because you would invoke the standard targets from the .btproj files. Other tasks, such as deploying, could be written simply by calling the builtin BtsTask command-line utility.
A lot of third-party tasks are available to help deal with BizTalk projects.
Please, have a look at this post on my blog for more informations.