In "Through the Looking Glass, Part 1", Mikhail's right eye socket is shown to be completely scarred over. This leaves no reason for him to be the owner of the glass eye.
However, Mikhail's eyelids could have been sewn together to avoid infection after the removal of his actual eye or the glass eye.
The Glass eye could have originally been acquired for Mikhail when he lost his eye, but since he decided not to use it. It is discovered in a box that is essentially used for storage by the tallies.
Malcolm - The police officer that Boone spoke to in "Hearts and Minds", (as Sawyer was brought into the police station in the background) possibly had a glass eye.
Radzinsky - Because the glass eye was found together with a missing splice of the Swan Orientation Film, it is likely that it belongs to the person who, according to Kelvin, removed the splice.
Radzinsky still has both of his eyes in 1977, but something could have happened over the next several years that caused him to lose one.
Mikhail could've lost his eye in a brawl or being tortured by Stuart Radzinsky while he explored the island trying to find the hostiles and Radzinsky left the glass eye in the Arrow as a clue for his encounter with Mikhail and gaining the information. Its extremely evident that Radzinsky had an extreme hatred for the hostiles and had a violent nature even though he was highly intelligent.
Because a prosthetic body part is unlikely to be left behind by accident, it is possible that something in the eye (or the eye itself) is of significance. For example, it is possible that its owner had to abandon it, or is now deceased. Alternate theories include the possibility that the owner had a miraculous organ regeneration due to the island's healing properties, or that the eye is merely a prop similar to Tom's fake beard.
The mural in the Swan hatch is a clue, because there is an image of a man with his left eye missing and crossed out.
As the mural shows both concrete and abstract concepts, the crossed out eye may be more indicative of spiritual blindness, rather than a removal of an eye, especially considering that one is white and one is black. The right eye of the figure is black, denoting nothing, while the other (crossed out one) is white, which is what most of the eye is. Also, the circle/dot although a sun symbol, may also literally be the eye (as we see many crudely-painted images such as stick figures, this may not be that far of a stretch). Again, this may be alluding to the spiritual blindness, since the blackened (not spiritually blind) side has the literal eye falling from it, but also, that eye takes the form of the sun. The Egyptian god Horus (fitting into the Egyptian culture featured prominently through the show) was also said to have the sun reside as his right eye (which is where the fallen sun/eye is oriented). This was a long way to say "the mural is probably symbolic".