The Apple App Store is not the only way to installation additional applications under OS X – another way is to install .pkg files (which have been created by the Apple Installer Framework).
Unfortunately not all applications installed using these files are present in the “Programs” category inside Finder. Uninstalling these applications using drag & drop inside the recycle bin is impossible.
But there is a tiny tool called General Package Uninstaller – it can be downloaded on GitHub. The program lists installed applications – and uninstalls them: