According to Safari's included keyboard shortcut list (in the Debug menu if you have it enabled, or via /Applications -> Safari.app -> (Control-click and Show Package Contents) Contents -> Resources -> Shortcuts.html), Command-. (Period) is for "Stop." However, if you open the Preferences window in Safari (Command-,) and then press Command-., it will close the preferences window.
[robg adds: You can also use Command-W or the Escape key to close the Preferences dialog, so there's really no reason at all to reach for the mouse!]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040603101425869