I was playing Skyrim recently and played a mage character with the white eyes. I decided to do the Dragonborn questline and noticed that his eyes had turned black. I though that that would be too cool to be true, so I dismissed it as light or some bug. When I had finished the questline I saw that the eyes were again white. I later did the Discerning the Transmundane quest and noticed that the eyes were black again before I opened the Oghma Infinium. After reading it I turned off the computer and when I restarted it today I noticed that the eyes were white again in the same place (and same light). I also remember Neloth commenting on the eyes after doing Dragonborn. What could this mean? The influence of Herma? I also remember him saying something about being in my mind.
Yup. Quite interesting, I know.