I think red font on black background will cause the least eyestrain from a quantum physics/chemistry perspective. Red has the least amount of energy and hence it's the least likely to hit electrons and to cause them to move into higher energy levels and to bounce them off into other atoms which tends to produce ions (and producing ions tends to cause unwanted chemical reactions). Red is basically the least destructive color which is why it doesn't destroy your film during development but other colors will. Same thing with your eyes, it's most likely the least harmful to your sensitive eyes just as well.
Also whenever something emits light it doesn't emit one color, it emits a distribution curve of frequencies. One of the reasons why CRT monitors and televisions were bad for your eyes if you sat close to them is that they emit more X - Rays than LCD monitors do. However, the color you see is determined by which frequency/frequencies are emitted from the light source and by the intensity of each frequency being emitted from the particular light source you are looking at. Light emitted from your LCD monitor (just like any other light source) does emit some UV and it does emit some X - rays, though with LCD monitors its not as intense as with CRT monitors. However, red light will tend to emit less ultraviolet and X - rays than white or purple light (since the intensity of red peaks at a lower frequency). and UV and higher energy radiation is more damaging than lower energy radiation. While stopping a light source from emitting harmful radiation is difficult it maybe possible to filter such radiation (ie: sunglasses do a good job filtering UV though they're probably not that ideal for a monitor).
Most of the light that we naturally see is reflected light, we hardly ever look directly into emitted light. Looking into a light bulb is bad for your eyes partly because you're not looking at reflected light, you're looking directly at emitted light. Likewise, looking into a monitor is bad for your eyes partly for the same reason. This is why a black background is optimal for causing the least amount of damage, you want to reduce the overall amount of light being directly emitted into your eyes (BTW, black is a shade, not a color). A black background will also reduce the U.V. and X - rays being emitted into your eyes.
and of course some common sense things to consider are to ensure that the brightness and contrast of your monitor are set appropriately (not too bright, not too dark), ensure you choose an appropriate font, font size, and monitor resolution, ensure you enable anti - aliasing and use something like cleartype fonts, and ensure that the room you are in has proper lighting.