So a long time ago I had to do a project that involved getting images from a scanner with an auto document feeder. It was a challenge doing this with WIA (Windows Imaging Aquisation) but I found some code somewhere online and made it into a nice library.
Today I finally shared this library with the world here: http://adfwia.codeplex.com/
[Update-15Dec2011]: I put it up on github too: https://github.com/gideondsouza/AutoDocumentFeed_for_WIA
It includes the source under the MIT License, it also has a little test app you can play with.
Note: Some scanners have trouble with the DIP setting. If you get:
Unhandled Exception : Value does not fall within range.
Try a higher or lower DPI.