Linux only: Previously mentioned F.lux has become a favourite among insomnia sufferers by tinting your monitor colour to keep it from being so harsh on your eyes. Free application RedShift achieves the same goal for Linux users.
You will need a little bit of command line work to get RedShift up and running, but it's nothing most Linux users can't handle. First, add ppa:jonls/redshift-ppa to your software sources list (through System > Administration > Software Sources in Ubuntu) and install RedShift in Synaptic. To get it running, you'll have to launch it from a terminal, with a few flags to let it know your geographic location (the new version is supposed to do this automatically, but it didn't work for me). Find out your latitude and longitude by clicking on the clock in the menu bar and editing your location. Ubuntu should give you your coordinates automatically.
Then, type the following command in terminal, using your latitude and longitude separated with a colon:
gtk-redshift -l 42.2:83.7
I found RedShift's default temperature levels much too extreme, so you can also edit those by adding the -t flag followed by the values (in the form of day:night). For example, for a more subtle change, you could try:
gtk-redshift -l 42.2:83.7 -t 6500:5500
You'll have to play around with the numbers a bit to find one that works for you. The lower the number, the more red it will get — 6500 being no tint at all. To make RedShift start up when your computer does, you can easily do so by going to System > Preferences > Startup Programs and adding a new program. Name it whatever you want type the above command (using your settings) in the command box.
Yes, F.lux does have a Linux version called xflux, and both xflux and RedShift have their quirks. What's great about RedShift is that you don't have to compile the source yourself, and it also has an icon in the menu bar from which you can quickly disable or quit it (for you graphic designers out there). Hit the link to check it out, and let us know what you think (or which program you prefer) in the comments.