I am a big fan of Evernote and use it to store all of my reference material (as explained in the GTD methodology). One of the key requirements to my online storage strategy is converting paper into PDF and getting it into Evernote as simply and quickly as possible.
A while back I found a free software called ScanDrop which did exactly that. I use it to scan paper directly from my Brother multifunction device and then upload it straight into my Evernote [For Google Docs users, it supports that service too] inbox ready for processing. It supports a whole range of scanners.
Main Window - Click to see full size
Cloud Service Selection Window
Did I mention it's free? Sure there are features missing but it meets 98% of my daily scanning requirements. They do have a Mac version but it costs $9.99 from the Mac AppStore (I still think it's worth it at that price).
I know some may be wondering how I use Evernote as my GTD reference system, I will cover that in a future entry.