This solution only works in version 9. Create a private stylesheet, and add style cells for any Section, etc., styles that you want to create using the following pattern:
Cell[StyleData["NonEvaluatingSection", StyleDefinitions -> StyleData["Section"]],
PrivateCellOptions->{"CellGroupBaseStyle"->{Evaluatable -> False,
Background->RGBColor[0.8, 0.8, 0.8]}},
MenuSortingValue->10000]
"CellGroupBaseStyle"
is new to version 9, and it allows you to layer in options to all cells which are grouped by the given style. So, in this case, we have a style "NonEvaluatingSection", which has all of the properties of the style "Section", except that it adds a background and Evaluatable->False
to itself and all of the cells grouped by it. The option is not documented, but that's just an oversight. It will be in a future release.
If, for example, you've added the above to the notebook's private stylesheet, then you can simply set the style of the head cell of any sections you don't want to evaluate to "NonEvaluatingSection" style (which you'll now see in the Format->Style menu).