System and Application folder locations

[eluser]tomdelonge[/eluser]
I always like to move my application folder to be even with my system folder. Is it a good idea to move both the system folder and the application folder out of the webroot? Basically just leave index.php, .htaccess, and images, css, and javascript? Does anyone else do that? I figure that way, there's less possibilities for someone to access the scripts.

Does it matter?