As a follow-on to Gruber today, there's at least one program out there whose outside-the-walled-garden version has features which the App Store version does not. Quoted from Optimal Layout's product page:
Optimal Layout fully supports Spaces: you can easily see which Space a windows is in. In the version purchased from this site you can also move groups of windows between Spaces with a keyboard command, note that this feature is not available in the version of Optimal Layout available on Apple's Mac App Store.
As an iOS App Store developer I wish I could say I was more excited about the Mac App Store, but balkanization such as this can't possibly bode well for the platform's health outside the walled garden.