Is there some way, e.g. through WMI, that I can query a box running IIS what web applications has been deployed to it using web-deploy?
Thanks in advance.
You can use web-deploy to -sync -whatif the whole server against a "standard" one, and that'll show you a list of differences.
If the Event Log shows Web Deploy deployments (does it?), and WMI can query the event logs, that might be more the level of detail you're looking for?
You did not mention what version of IIS, but have you checked out the MSDN documentation on managing IIS via WMI?