Terminal commands for "Application Windows" and "Show Desktop" in Mountain Lion
You can execute "Mission Control" with specific arguments to trigger the behavior that you desire:

Mission Control:

/Applications/Mission\ Control.app/Contents/MacOS/Mission\ Control


Show Desktop:

/Applications/Mission\ Control.app/Contents/MacOS/Mission\ Control 1


Application Windows:

/Applications/Mission\ Control.app/Contents/MacOS/Mission\ Control 2


Alternately, you could use osascript to execute the key code that you have setup for "Application Windows" and "Show Desktop". In the example below, I have "Desktop" mapped to the F8 key, and "Application Windows" setup to use F9. The key codes for these F keys can be found in various places.

osascript -e "tell applications \"System Events\"" -e "key code 100" -e "end tell"

osascript -e "tell applications \"System Events\"" -e "key code 101" -e "end tell"