I'm no expert on this, so feel free to correct any errors... First of all, this seems like a DAM (digital assets management) issue more than a content management issue. So, perhaps looking in that direction may be of assistance.
I think this is normally called document imaging. I'd suggest using any non-proprietary format that won't be depreciated in the near future that the automated scanning device can use. Whatever will ultimately save you time. PDF/Tiff will most likely work equally as well. I wouldn't consider GIFs or JPGs good formats for archiving printed documentation, though I'm sure you could auto-convert better quality archive formats to those formats for dissemination via the browser. As for the quality differences in the different formats, that's really a lesser issue compared to the resolution everything is scanned in at. -Darrel -- http://cms-list.org/ trim your replies for good karma.
