Like you, I have also been trying to reduce the amount of paper in my home office. I use an HP ScanJet 4570C (Flatbed USB2). I absolutely HATE the HP Scanning software they included with this! However, one evening I discovered a program called Microsoft Document Scanning. I'm not a big fan of Microsoft but since this is part of Microsoft Office, I figured that I might as well use it. It provides a much better "front-end" to the scanner.
When I scan documents with this program it saves them as TIF files. The program uses OCR to convert the text on the scanned page and stores it in the TIF's header. This means that the files are perfect copies of the originals but are still searchable using the Windows "Find" feature.
The TIFs are typically smaller than a PDF file, expecially if the original document has any graphics.
The advantage over JPEG or GIF is that the text is stored in the file to make it searchable.
The advantage over PDF is that the integrity of the original paper document is maintained. In a PDF scan, if the OCR doesn't read something exactly right, then I don't have an accurate copy of the original. Imigine that if I scan in all the invoices from my clients and save them as PDF. If the OCR didn't read a number right, I couldn't use this as a valid document in any dispute.
Good luck in finding a solution that works for you! I just wanted to put my $.02 in here.
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Thanks,
Ricky