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There's an ongoing discussion about this on the Homebrew Robotics mailing list: https://groups.google.com/forum/#!topic/hbrobotics/TrasImSJxjU

The bottom line is that this should be doable, provided that you choose a motor shield and encoder shield that are compatible with one another. Mostly this just means that they shouldn't use the same pins, but you may also want to check that they don't use the same timers and hardware interrupts.

From there, you'll probably need to update the arduino sketch for your shield(s) pin configuration.