Here’s one reason to use Evince, a free software PDF reader alternative to Adobe’s reader (besides the huge fact that Adobe Reader is a proprietary, non-free pdf reader and doesn’t respect your freedom…): With a simple click on the “Inverted Colors” button from the View Tab in the Toolbar, you can now be kind to your eyes (and to the environment for not printing out the PDF) by viewing white text on black background!
UPDATE March 5, 2013: Evince really is great for viewing pdf’s. If you are interested in more robust note-taking/annotation(s)/commenting, etc., check out my post about Okular (and even Xournal) for GNU/Linux. Okular also works for Windows (and Mac), I think. There is another post on inverting screen colors for the whole system using Xcalib.