Cmd-K (the default shortcut for Safari -> Block Pop-Up Windows).
The obvious thing to do would be to go to Keyboard & Mouse -> Keyboard Shortcuts in SystemPreferences and set the shortcut to none - which is unfortunately not possible AFAIK.
The next thing that comes to mind is setting the shortcut using the default command in Terminal - which unfortunately was broken in this regard until recently and would interpret a UserKeyEquivalent of nil as just l, which isn't what we wanted.
The good news is that it must have been fixed in one of the latest system updates, so here's how to remove the shortcut from Safari -> Block Pop-Up Windows in Terminal:
defaults write com.apple.Safari NSUserKeyEquivalents -dict-add "Block Pop-Up Windows" "nil"
Note that us usual, this must be entered on a single line in Terminal. And of course you can use the same technique to remove shortcuts from any other application.

