Install ccsm (compiz config settings manager) and compiz plugins:
sudo apt-get install compizconfig-settings-manager
sudo apt-get install compiz-plugins
In CCSM, enable the Opacity, Brightness, Saturation
Plugin. In that plugin, you can reduce the saturation (I myself make saturation zero and use invert plugin to invert colors (white on black is less strenuous on eyes when casual reading/browsing) generally to reduce eye-strain :))
To use the OBS plugin, simply make a New rule which can be used to match windows by name, type, class, etc. For example, to match all windows, use type=any
Screenshots:

