Fujitsu has recently done a video that shows how you can use a highlighter (yes, a real physical highlighter) with a ScanSnap S1500 to choose which parts of a document you want to be searchable.
Basically, you go into ScanSnap Manager and check the setting “Set the marked text as a keyword in the PDF file”. Then when you scan it in, it will detect which parts of the documents are highlighted.
Unfortunately this only works on black & white documents, but still pretty cool.