On my laptop, I've been using f.lux [0] to prevent the bright monitor lighting from keeping me too alert late into the night. It took me a while to get accustomed to the hues, but I really like the way the light softens as the evening progresses.
There is also Redshift [0][1], which I've found easier and simpler to use/install on Linux (but I've researched f.lux long time ago, so things may be different now). I remember that at first I couldn't stand that everything was kind of orangeish, but after a while I honestly didn't notice it anymore. From my personal experience, I can tell that it really made my eyes suffer less from long sessions of copmuter use.
[0] http://jonls.dk/redshift/ [1] https://github.com/jonls/redshift