On Linux I use the 'Negative' Compiz plugin. You can apply it on a window by window basis or desktop-wide. For both modes there are keyboard shortcuts (that's what makes it such a killer feature IMO). People find the screen weird when I enable the plugin but I'm a practical guy and this has saved my eyesight.

I know you can invert colors in OSX but the effect is desktop-wide and you can't use a hotkey to enable or disable it. Does something similar exist for other OSes?