Two days ago I installed the latest Arch Linux x64 + Xfce. Eye strain, if any, is very minimal. No headaches. Probably the best desktop distro, in terms of eye strain, I have tried so far. This is great.
Out of the box, "nouveau" driver, Nvidia Quadro NVS 295
I currently tend to believe the font antialiasing, as mentioned in other threads, is indeed causing some extra eye strain. I disabled it completely now and will continue to use Arch Linux for the next days.
I can even use Chromium (even hardware-accelerated), which definitely hurt under Windows.
Arch Linux is known to always have the latest packages. Maybe other distros will soon be more eye-friendly, too.
vinkenvvt, did you have eye strain before with other Linux distributions?