Visual Studio lets you create project templates, which have certain files and directories already in them when you create a new project. Trouble is, the documentation for this is a little haphazard.
You can find documentation on the objects available to you in the 1033\default.js file in these MSDN pages.
For creating new Project Templates, you can have a look at this tutorial, which also links to some more MSDN information.
I'd recommend just copying existing Project Templates and then altering them for your nefarious purposes. I'm planning on creating a slightly more advanced Project Wizard soon, so I'll post instructions on that process as well.