I had to do this when my wife and I moved from Austin, TX to London. My wife and I turned 2 filing cabinets worth of files into a dropbox directory tree. For the actual scanning, I followed the wirecutter's advice and found that the Fujitsu ScanSnap S1300i Mobile Document Scanner worked well. It seems they are now recommending[1] a different scanner though.

For the actual organization, we had a naming scheme of "$(source of document) $(title) $(date %F).pdf". For example: "Texas DMV Toyota Sienna Registration Receipt 2015-05-16.pdf

[1] http://thewirecutter.com/reviews/best-portable-document-scan...