pdf / djvu tools

PDF
http://www.sejda.org/download/ —console library
http://sourceforge.net/projects/pkpdfconverter/ —extract to images & more
http://pdfsam.org/ —split and merge (& more)
http://download.pdfforge.org/download/images2pdf —images to pdf (other tools available at pdfforge); not very much trusted
http://sourceforge.net/projects/ttrpdftojpg/ —another pdf to jpg (& other image formats)
http://sourceforge.net/projects/image2pdf/ —another images to pdf
http://sourceforge.net/projects/pdfcreate/ —another images to pdf
http://www.djvu-soft.narod.ru/soft/mupdf_bin_r1309_16_07_2009.rar —MuPDF utils (console pack)
http://sourceforge.net/projects/briss/ —cropping PDF
http://code.google.com/p/papercrop/ —another solution for cropping PDF

Scan processing
http://scantailor.sourceforge.net/

DJVU
http://www.djvu-soft.narod.ru/soft/djvu_small_v0_4.rar —create
http://www.djvu-soft.narod.ru/soft/djvu_imager_v1_5.rar
http://www.djvu-soft.narod.ru/scan/djvu_imager.htm —handle images
http://www.comicer.com/stronghorse/software/exe/DjVuToy_eng.zip —DjVu Toy, DjVu (quasi)direct editor
http://www.comicer.com/stronghorse/software/exe/PdgCntEditor_eng.zip —bookmark editor for PDF & DjVu