My real worry is that programs like those will stop being made. My secondary worry is that more and more features of the OS will require being a signed application by Apple. i.e. only work from the MAS. Consider iCloud. It’s completely understandable why Apple may wish to have applications go through the approval process to use iCloud. (Apple apparently hasn’t decided on policy here yet – at least not in any official statement) Suddenly that means that no application can send arbitrary Applescript and access iCloud. I think it is safe to say that more and more features may start requiring the limits that the app store imposes.
John Gruber also notes the uncertainty:
My gut feeling/semi-informed hunch is that yes, it will be restricted to App Store apps, so that Apple can approve all iCloud storage use cases in advance, and easily pull the plug on any app that proves to be abusive in the wild. Put another way, my bet is that if your app isn’t signed by Apple, it won’t be able to write to an iCloud container.
iCloud and the application sandbox were probably the two biggest Mac announcements at WWDC in June. Now they’re deployed on customers’ Macs, and Apple still hasn’t clarified the policies for using them.