I scan in most of my mail, and convert the images into multiple page PDF files. This was fine under Linux, and I had a shell script using ImageMagick to do this.
But with moving to the Mac, this wasn't so easy. The original script drove the scanner and that seems to be the sticking point. I've farted about with various Darwin Ports etc of the SANE and TWAIN packages with nothing reliable.
I'm now using Vuescan to drive the scanner, and I've written a Java application that takes a bunch of graphic files and creates a PDF with one image per page. This application is called Image Funnel.
Screenshot here:
As you can see, it allows you to set a number of options for the document, such as author, title, subject and keywords. It also allows you to set different types of encryption and permissions on the document.
Currently I have it packaged as an OS X application and it can be downloaded from here. (NB: it's 1.8MB).
In the next few days (probably weeks due to Christmas) I'm going to set up a project for it on sourceforge.net.