>ePub supports color configuration (FBReader). Not sure about pdf.
At least Okular is able to change the colors of pdfs, background and foreground. It's hands down the best pdf reader in my book otherwise too. Real fullscreen and scrolls like a dream. (If you do try it and have problems with audio afterwards, it could be the knotify daemon it loads when playing a sound interfering. You can make the knotify binary non-executable to prevent any such trouble.)
