I scan to tif instead of pdf. the pdf format changes a little between versions and I sometimes have older pdf's throw errors with newer readers. Its also easier to make images into pdf's than it is to convert a pdf into something else.

When it comes to scanned documents I find that showing due diligence tends to go a long way. If you produce one single scan of something important that tends to look like it was produced for the situation. But if you show a nicely organized set of everything scanned then it becomes more believable that it is legit.

Certain exceptions will apply of course.

Scans also help to make it easier to replace originals. If you call up for a replacement someone will need to know how to find the original in their database. If you can call up and say I need document number 123435 dated 2009-11-17 that is 20 pages in length they can find and replace it quicker.