I've successfully done automatic snapshots from an Ubuntu instance on AWS using a bash script and the API tools. But how is this done with a Windows Server instance? Is there a similar set of tools available?
You can use the EC2 API tools on Wndows; here's a useful link with some details.
To replace your bash script, you're better off using a scripting language like Perl or Python that's supported on Windows, or you could look into PowerShell.