I found that the only thing preventing me from assigning command-tab in Contour's setup utility was the system-wide application switcher itself. So using information from hints (here and here), I came up with a step-by-step guide that should allow you to set these commands without having to restart your computer.
You could also follow this procedure to enter command-tab in any utility that depends on "sensing" your keystrokes to set its shortcuts.
- Launch Contour Shuttle Utility
- Launch Activity Monitor
- Launch Terminal
- Copy these lines to Terminal (don't copy the $):
$ cd /System/Library/CoreServices/ $ sudo mv Dock.app Dock.app.deactivated - Hit return, type your system admin password, hit return again
- Select "Dock" in Activity Monitor
- Click "Quit Process" and confirm quit
- Switch to Contour Shuttle Utility
- Set all of your preferred buttons for command-tab, command-shift-tab, etc.
- Switch back to Terminal and copy this line:
sudo mv Dock.app.deactivated Dock.app - Restart the dock (by clicking on its application icon or by logging out)

