They indicate that the app was recently updated and has not yet been launched since the update.
The pale blue dot will appear either if iOS 7 updated the app with Automatic Updates or if the user updated it manually.
In iOS 6, when you installed a new app, its icon would display a small "new" banner across one corner. In iOS 7, new apps are represented by a blue dot.
That dot also appears when you update an existing app (or the OS updates it for you in the background). In both cases, the dot disappears after you launch that app for the first time.