One of my better purchasing decisions last year was to buy a ScanSnap scanner. What makes this scanner great is its ability to quickly scan both individual pages and stacks of pages (up to about 30-40) and the fact that it automatically scans both sides of pages that go through the unit. Scanned documents are automatically saved as PDF files.
One issue I have been having while scanning documents whose pages had been stapled together is having the pages “stick together” after the staple has been removed. This behavior is apparently the result of the stapling or the staple-removing process. As the ends of the metal staple are forced through the paper (or drawn back through the paper when a staple is removed), small, nested cone-like structures are created along the paths of the staple holes. When the staple is removed, a number of such structures will retain enough purchase to cause pages to all too often go through the scanner two at a time. The only way, then, to ensure glitch-free scanning of such documents is to first page through and manually separate the pages, which takes some time.
Or you could try my quick and dirty solution.
Unless there is an overriding reason to retain the entire page of the document being scanned (and this is hardly ever the case, as documents are stapled in the corner, away from text or graphics), just cut off the stapled corner of the document. Most of the time, the missing corner won't even show up in the scan.