The best way is to use one of the “Shutdown POPFile” links. One of them can be found in the POPFile Control Center, the other can be found in the start menu if you are using the windows version of POPFile.
POPFile will also close down gracefully if you shutdown or reboot your computer.
Windows users can also use the program, stop_pf.exe, installed in their POPFile directory to stop POPFile from a batch file or the start run dialog.
WARNING: You should only resort to “killing” POPFile with the Windows Task Manager or the *nix kill command if you are really desperate as this may lead to a loss of configuration settings or, even worse, a damaged corpus.