I don't speak from personal experience, but you might take a look at graphics/ocropus. According to Wikipedia, "It aims primarily for high-volume document conversion." I've been wanting to try it out for a while now, but haven't had the chance yet.
There is also graphics/gscan2pdf which can use ocropus for OCR. Unfortunately, the current gscan2pdf port has given me problems on FreeBSD (it crashes a lot).
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