I like DEVONthink. While I don't have a scanner, it has been highly recommended by folks who use it to scan and organize paper documents.
DEVONthink stores your documents,
scanned papers, email messages, notes,
bookmarks, etc. in one place. Access
live web pages seamlessly from within
DEVONthink to review, extract further
It does cost money, $50 to $150 depending on which edition you buy. I got a free copy of "Personal" through a MacHeist promotion, but I would definitely buy a copy of it if I had to. They have a download trial version so you can give it a go.
After revisiting this topic, it seems the common ground is DEVONthink Pro, and the Fujitsu ScanSnap (model 5500 is mentioned often for Mac users). Here's a blog post with some more information. You can probably find more information than you want by searching Google for "scansnap devonthink". When it fits in the budget, I'll be going this route.