MacOS – Set keyboard shortcut for nested menu selection

The following Applescript will trigger the zoom button (that´s button 2) in the frontmost application´s window. You could make this a service and define a global shortcut for it or use an application like quicksilver to call it.

tell application "System Events"
set frontApplication to (get name of every process whose frontmost is true) as string
tell process frontApplication
    click button 2 of window 1
end tell
end tell 

Many applications like Terminal also have a menu item like Window > Cycle Through Windows. It stays assigned to ⌘` even if you change the shortcut in the Keyboard & Text Input preferences.

You could add a custom shortcut for Cycle Through Windows in the Application Shortcuts preferences, or disable it with defaults write -g NSUserKeyEquivalents -dict-add "Cycle Through Windows" nul.

You could also force TotalTerminal to use ⌘` by editing ~/Library/Preferences/com.apple.Terminal.plist directly.

<key>ToggleVisor</key>
<dict>
    <key>KeyCode</key>
    <integer>50</integer>
    <key>Modifiers</key>
    <integer>9437184</integer>
</dict>