What do Jonas' and Gabe's eyes represent?
No one in the community can see color, but they can see shades of lightness and darkness, and the eyes of Jonas and Gabe are light, unlike everyone else in the community, all of whom have dark eyes. We can infer that Jonas and Gabe have blue, green, gray, or hazel eyes and that everyone else has brown eyes. Because of Sameness, this is clearly an anomaly, and that anomaly seems to symbolize a deeper difference in Jonas and Gabe, a difference that is not clear until later in the story.
Sameness is a ruling principle of the community, even to the degree that people should look the same, but the community has not been able to successfully breed out all differences. Fiona, for example, is a redhead, which we know because Jonas compares her hair color to the color of an apple, after he begins to see colors. His eyes and Gabe's eyes are another example, but it is considered rude to comment on differences, and Jonas has no real reason to think his and Gabe's eye color are particularly significant.
However, Gabe turns out to be the only person to whom Jonas can transmit any memories, without even trying. He has tried to transmit memories to Lily and his father, but this has been completely unsuccessful. This suggests that there is some relationship between eye color and the ability to receive memories, and it may very well be that this was the basis of the choice of Jonas as the Receiver. We do know enough about genetics to know that traits are sometimes "bundled" together, and this makes this a plausible interpretation of what the eye color is meant to represent in the story. When Jonas runs away from the community to Elsewhere, his choice to take Gabe is not only to rescue him from release, but also because Gabe is the only person with whom he can share memories. Gabe is his soul-mate in some way, and there might even be a biological connection, since Jonas has no way of knowing who his or Gabe's birth parents were.
Thus, the light color of Jonas and Gabe's eyes represents a departure from Sameness and it is reasonable to infer that their eyes also represent the ability to receive memories. They do not fit in to the community, and throughout the entire story, the stage is being set for their leaving.
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