I have a large number of PDF files which have two slides to a page (for printing).
The format is A4 pages each with two slides setup like so:
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Briss is "a simple cross-platform (Linux, Windows, Mac OSX) application for cropping PDF files. A simple user interface lets you define exactly the crop-region by fitting a rectangle on the visually overlaid pages." It's open source (GPL).
Works well for me. The GUI is minimal, but functional. It can also be used from the command line.