As for storage, we support two modes in our application, file based, and database integrated.  Obviously the file based means that the scanned files will be stored on disk in a folder.  We use the patient PK as the folder name to store in a shared location.  However, we highly prefer and recommend database integrated.  You will want to use a VARBINARY(MAX) field and allow the file to come in a standardized format.  Depending on what you need to do with the  file long-term, there are different options here.  The MOST important thing that I will tell you is to optimize the file in your code for size.  In our application we allow the file to be optimized to a size no larger than 3 MP and we default it to 1.5 MP.  Most people will leave settings wide open on a scanner and the image will come in so big it could wallpaper your whole house if you printed it out!!  As for the image type, it depends on the quality that you need, but we tend to use PNG a lot for both a quality and size combination.  You can play with this and your needs though.  In fact, in our application, we will store PDF for documents being scanned in, as well as Word DOCs and pretty much any other file format you can thing of.  When scanning in PDFs, however, be sure to optimize the image before dumping it into a page just like you would a standard image file.