ScanTailor - Scan Tailor is an interactive post-processing tool for scanned pages.
PDFTK Builder - PDFTK Builder is a free graphical interface to for PDFTK, making it much easier to use.
Briss - Cross-platform application for cropping PDF files in a simple and fast way via a GUI.
QPDF - QPDF is a command-line program that does structural, content-preserving transformations on PDF...
ScanKromsator - Scan Software with several advanced options
PyPDF2 - PyPDF2 - A utility to read and write pdfs with Python