I'd love to try out f.lux but I am a little wary of installing a binary that messes with my xwindow settings. I wish the source was available...
IIRC redshift was the most developed of them when I looked into it a while back.
http://alternativeto.net/software/f46lux/?license=opensource
dfc@ronin:~$ apt-cache search redshift
gtk-redshift - Adjusts the color temperature of your screen with GTK+ integration
redshift - Adjusts the color temperature of your screenIssues highlighted in the FAQ page here. http://stereopsis.com/flux/faq.html