For some reason, it never occurred to me that the perfect way to store a set of scanned documents is in a PDF
file. As a card-carrying nerd, bitmaps (TIFFs) of scanned pages always worked well enough. But when my non-technical attorney stuffed a bunch of papers in a machine scanner and emailed me a nicely completed PDF file, I realized what a great solution this is. No file format issues, easy to email, easy to print, and easy to bundle multiple pages. And best of all, easy to do in Linux.
If you have a scanner properly configured in Linux, just use the scanimage app to grab pages from the scanner in the native .pnm file format.
scanimage --resolution 150 --mode grayscale > page1.pnm
Then, just use the ImageMajick tools to convert the scanned pages to a PDF file.
convert *.pnm scannedstuff.pdf
It couldn't be easier. For more variants of this tip, along with some sample scanning scripts, check out this blog entry: http://www.megginson.com/blogs/quoderat/archives/2006/01/26/scanning-to-pdf-in-linux/