I left a comment on Gene's blog and we had a short discussion there.
I scan printed materials directly to PDF. I use
CutePDF Pro which lets me merge different PDF files. CutePDF Pro also has editing features such as adding notes, comments, and text boxes, too. There's also a "reduce file size" feature. So does Adobe Acrobat, altho I'm not sure if it's available in both the regular and Pro versions, or just the latter.
Unfortunately, CutePDF is only available for Windows.