Linux: Linux is fully capable of scanning, processing and otherwise working with PDF documents, but some of the default tools aren't exactly new-user-friendly. PDF Mod is a straight-forward tool for adding and subtracting pages, exporting images, and other document tweaks.
The software, written in just over a week last month, lays out all the pages of PDF in a grid, then lets you click on a page to rotate or remove it. You can select even, odd or matching pages throughout a PDF, extract images from a document into a folder, and re-save your document as a new, fixed PDF. That's all it does, but for those whose spirits droop a bit when faced with the myriad options and buttons in XSane or other PostScript/PDF tools, you'll dig PDF Mod's simplicity.
PDF Mod is available as a free source package for Linux systems that's fairly easy to compile; the Lazy Ubuntu blog linked below has a copy-paste terminal guide for Ubuntu users.