In the past the Executive Branch would implement to their best of their ability the specific funding actions in the various appropriation bills passed by Congress. One of my jobs when I worked for the Air Force acquisition office was to track all of the specific program additions, commonly called earmarks. Due to the way the laws were written these were primarily specified in the Report, usually the House bill, not in the actual text of the law. If you look at the appropriation bill status on Thomas.loc.gov you will see this. The reports are called HR.
President Bush, to protest the addition of large number of unrequested earmarks in the omnibus appropriations bill just passed by Congress says that the Executive Branch will not implement those only contained in the Report, as they are not legally binding. If he does this it will be huge. He has found a way to prevent the money being spent.
I know that we would search for a way to legally execute the money, and sometimes could not. Anyway a good discussion is here at Captain Quarters: Will Bush Cancel Congress' Christmas? (Bumped)