Remove applications from Software Update
Somebody asked about it on Apple Discussion Groups here. The answer is:

For the software update you would like to hide - make sure the full description of the update is shown - click "More..." if needed to show the full description

Right click on the update window.  Select "Hide update"

This will hide the update and it will not show in the App Store Updates Window or counted on the dock icon.

To restore - select "Show all software updates.." which is now shown in the App store "Store" menu.  Then "Reload Page" from the Store menu.