I know that this is an issue for me, so I try very hard to eliminate the amount of paper or documents that I have to keep track of by dealing with incoming documents as quickly as I can.
One app that has been immensely helpful for me in this area is TurboScan. Using the camera feature on my iphone, I can scan documents into an image or PDF file immediately.
If I have a document that may be helpful later as a reference or I do not necessarily need to have in a hard copy, I can just set it down on the table, scan, and save it. TurboScan allows you to adjust the brightness and a variety of other settings directly within the app. It's really easy to use!
The best part is that I can automatically email the document to my Evernote account and it is saved!
This app is available for purchase in the app store for just $1.99. A steal, to be sure!
Check it out!