Hi:
http://gscan2pdf.sourceforge.net/
It is a gui to several cmd line utilities, including scanning tools.
BUT the wonderful thing is that you van import a scanned pdf and clean it through unpaper (
http://unpaper.berlios.de/). So you will be able to automagically:
-Clean dark/gray areas
-Remove isolated dark spots
-Correct unaligned lines
-Dither
You can also split a double column document or crop a document, the whole document or page by page.
The processing can be done sequentially i.e. first split then crop then clean.
After processing you can save it in several formarts, pdf, djvu or individual images of the pages.
The interface can be confusing at first but with a bit of practice it is pretty straightforward..
Regards.