Like Gabe, I have my ScanSnap import to Evernote by default. Beyond the ScanSnap itself, the key to keeping my scanning workflow as easy-to-use and frictionless as possible is maintaining an “Inbox” notebook so I can decouple the scanning and processing stages of my workflow.
With a dedicated Evernote inbox I can quickly scan in several document sets, then figure out what to do with it all (what to call the notes, what to tag them, where to file them, etc.) at a more convenient time – usually “later”. If you find yourself being lazy like me and leaving a lot of time between processing periods, Evernote’s OCR saves you by allowing full search of the PDF whether you’ve figured out where to file it or not.
This kind of search (especially while mobile) is what makes Evernote practically irreplaceable for me.
Like Erik, I also have “legacy” ScanSnap, but I’m not an Evernote user. I like batch processing as well, so my ScanSnap just dumps the OCRed PDFs into a folder within my Dropbox that I’ve set up to act as an inbox.
Incidentally, the Fujitsu scanning software can be set to OCR after each scan using ABBYY FineReader, which Fujitsu includes with the ScanSnap. You can also use FineReader to OCR your PDFs in batches later, and the accuracy is very good either way. What I like is that the OCR data becomes a part of the PDF, making it searchable by more than just Evernote.