New, updated tutorial available
Please use the new Preparing Geometer’s Sketchpad for Munki instructions instead of the ones below.
Generally with licensed software, the trick with importing into Munki is to get the normal software imported and then import as an "update," whatever needs to happen to get it licensed.
Geometer's Sketchpad works that way. So you import the Sketchpad app as you would any other. Then activate it on one computer and find what's in ~/Library/Application Support/The Geometer's Sketchpad (by default, Sketchpad seems to activate for only the logged-in user—I got a message about how you have to launch it as administrator if you want it activated for all users, even though I was using an administrator, albeit not root, account).
Inside that folder, you should see two files: licenseK.plist and reference_licenseK.plist.
Just take the entire folder and set it up (you can use Packages) to distribute the folder to be in /Library/Application Support/The Geometer's Sketchpad.
Import that package into Munki as an update for Sketchpad, and you should be all set.