ScreenNinja allows you to specify which apps will be visible and which will be hidden from your recordings or screenshots. When you hide an app with ScreenNinja, the app will still appear on your screen and you can use and interact with it as usual. However, hidden apps won't appear in your recordings or screenshots.1
Some apps are not listed in ScreenNinja's App Visibility Panel. Apps that aren't currently running, apps that live in your Menu Bar (like Dropbox or Alfred), and other background processess that don't generally show a UI won't appear in the App Visibility Panel. But, you can drag the icon of any Mac app from the Finder into ScreenNinja's App Visibility Panel to add that app to the list, and control it's visibility.
You can also control the visiblity of System Elements such as the Menu Bar, System Menus (Including Menu Items, Context Menus, etc), Desktop Icons, The Dock, Mouse Cursor and Notitification Center popup notifications.
Hiding apps (such as web browsers or IM clients) or System Elements (cluttered Dock and Desktop Icons) can be useful for removing personal information and other distractions from your screencasts.
The icons and/or names of hidden apps may still appear in your Menu Bar, Dock or in the Finder. You can hide these elements separately. ↩