Tinderbox (http://eastgate.com/Tinderbox) -- and DevonTHINK Pro Office (https://www.devontechnologies.com/products/devonthink/overview.html): neither has a satisfactory equivalent on Windows or Linux and if you've invested any time in either of these, then a move away from the Mac is very difficult.
I'm sure this comment will be of limited use, but if you're on a Mac, try DevonThink. :)
A few years ago I invested in a Fujitsu ScanSnap iX 500, and it's been awesome. It should work with a lot of different packages, but DevonThink has very good support for it. I've got years worth of documents, and they're easy to find; I've been very happy with DT (I also turned my Dad onto it, and he loves it also -- and he's hard to please). It's also not very expensive (one time, ~$150, updates are included).
Honestly, though? The scanner is IMO far more important than the software. The work of scanning is the hard part. The ScanSnap makes it far, far easier than using, say, an HP all-in-one. It's a night-and-day kind of difference.
You can always change the software; re-scanning everything would suck, though. :)