Here's a great find recommended to me (and all polyphasic sleepers) by one of my co-presenters at Penguicon, the very well-mannered and well-researched Neil Funk.
I've used it for several weeks now and WOW, what a difference. F.lux runs in the background, and on my machine uses next to no resources and has never caused any conflict or problems.
What it does is adjust the "temperature" of the colors on your screen — making them look less blue and more orange. You tell it a "daytime" and a "night-time" setting, and it switches them at sunset and sunrise automatically.
Two things: Bluer light makes your eyes more tired. And temperature is something that you adjust to remarkably quickly — within a day, I had to try to see the difference; and after a week I turned f.lux off and found the resulting color blinding and unbearable.
My eyes have been less tired by a good measure overall since I got this software, and I'm calling it a great find for polyphasers everywhere!