I am going to say this first. This is a theory... actually, at this point I'm reluctant to even call it a theory at this point. It has very little evidence to back it up, however, from what I have seen, virtually no evidence to disprove it. So, at the moment, I am just going to call this "speculation".
This is based off of one of my theories/hopes for what happens in DLC 3 & 4, and will most likely be either proved or disproved in those maps.
First, my over-generalized summary of eye colors and what they signify.
Yellow: Apothicon control or influence
Blue: Vril-ya control or influence
Red: Ancient Evil control or influence
Orange: Unknown/Maxis
Green: Turned Zombie (quite possibly just for gameplay)
Now to elaborate on the more outrageous implications of this over-generalization.
Yellow: This would imply that Samantha was influenced by Apothicon forces. That is the MOST controversial claim in this. However, although there is no solid evidence for this, Sam did go from crying and being a normal girl to laughing maniacally and being demonic and sadistic VERY quickly. Just something to consider along with the timeline implications of certain maps possibly happening before Samantha taking control.
Blue: Richtofen... Remember those voices in his head? The voices he suddenly had the second he touched an ancient vril machine? Just food for thought. Also, the abundance of blue-eyed zombies in the crazy place and the "crusader" zombies with the Keeper symbol on their robes.
Red: Seen throughout MotD and now Gorod Krovi (very peculiar). In MotD there is clearly some entity controlling what is happening. I absolutely do NOT believe that this entity is Brutus. Why would Brutus talk about how he was trapped there "just like you" if he was in control? He would either leave or be there willingly. I am expecting/hoping for some elaboration on the red eye color in Gorod Krovi.
Orange: Seen only when Maxis' end game in Buried is achieved. Possibly an uninfluenced Maxis in control? Not expecting an explanation or any hidden reason to be behind this.
Green: Turned AAT Zombie. Probably just for gameplay, but I would LOVE IT if Treyarch actually put a storyline reason for this in the game.
So, I will add onto this as new information comes up. Let me know what you think of this speculation/far-fetched "theory?". Also, feel free to ask about specific times were this doesn't quite make sense and I will elaborate.