Like you, I spend long hours at the computer, including many late nights. Almost all the applications that I use have a white background, and staring at the bright screen all day can be pretty hard on my eyes.
I’ve tried changing the Windows display settings, to choose a different background colour, but haven’t found anything satisfactory. Light greys and blues are easier on my eyes, but don’t provide enough contrast, so I strain to read what’s on the screen.
Today I discovered that I might have the brightness level too high on my monitors. My setting was about 80, but the calibration information at the Photographer USA and Display Calibration sites suggest a lower setting. I’ve lowered my brightness settings to about 55, and things seem better already.
How bright is your monitor? Can you lower the setting to save your eyes?