Little Snitch consists of multiple components. It is therefore essential to run the Little Snitch Uninstaller to make sure all components are removed from your system. Little Snitch automatically starts the uninstaller as soon as you move the Little Snitch Configuration application to the trash. Alternatively you can start the uninstaller manually from /Library/Little Snitch/Little Snitch Uninstaller.app.
The uninstaller lets you choose whether to remove or preserve user specific data (like rules and settings). If you want to remove those items manually, delete the following files and folders (the “~” tilde sign refers to your home folder):
/Library/Application Support/Objective Development/Little Snitch/
~/Library/Application Support/Little Snitch/