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For output format I use either jpg or tif, and I found out that it looks better than bmp and easier to manipulate if you do not want to ocr but build yourself a picture book which can be read by anything that reads embedded pictures (Fbreader, Ebk1150...)
For ocr'ing text grayscale does not work well for me, b&w is crisper and ocr's well. For covers or stuff with pictures like documents, diplomas... grayscale is indeed better. Since I have a b&w laser printer only, color is not that useful for me (though sometimes it enhances some documents, but scanning in color is very slow).
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