I have found this particularly helpful because it contains a deskew option to straighten crooked scans, and can make the PDFs searchable using OCR
NAPS2 is a document scanning application with a focus on simplicity and ease of use. Scan your documents from WIA- and TWAIN-compatible scanners, organize the pages as you like, and save them as PDF, TIFF, JPEG, PNG, and other file formats. Requires .NET Framework 4.0 or higher.
NAPS2 is currently available in over 30 different languages. Want to see NAPS2 in your preferred language? Help translate! See the wiki for more details.
This is a fork of the NAPS project with many improvements.