In the Desktop version of Adobe Reader (at least version 9), you can go into Edit > Preferences > Accessibility > Replace Document Colors > Custom Color, and then set (Page Background = Black) and (Document Text = White).
But this isn't really relevant for most portable devices, and I don't know what PDF viewers are or will be available for the iPad -- I imagine it'll be the same as for iPhones, which as far as I know, doesn't include Adobe Reader.
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