What I love most about this site is the way it is carried on by theory contributors. Awesome work, guys! Anyways, I finally got back to thinking about Potter & Co., which led me to the information concerning Harry's eye color. We know that is important; that fact has been solidified by JKR herself. Why, though, do they hold significance, and to whom?
I believe that Harry's eye color is important for the sole purpose of Snape's "redeeming process," so to speak. The only emotions towards Lily (as well as James) that Voldemort possesses is loathing, so Harry having his mother's eyes would not affect him, not in my opinion, at least. Anyways, back to the main point...
Let's face the facts: Snape loved Lily. For this reason and this reason alone, Snape is going to impacted by Harry's emerald green orbs (poetic, no?). Imagine this: Snape is looming over an injured Harry, grinning fiendishly whilst raising his wand to deliver the most traitorous blow ever received by the young wizard. All of a sudden, as the former Potion master's lips part to release the "magic" word, a light shines down on Harry, illuminating the verdant green of Potter's eyes. Snape stands in bewilderment as his surroundings fade to black and Harry's face is replaced by Lily's, the bright eyes remaining the same throughout the transformation. "Severus," Lily whispers gently, "this is not the way." She reaches out to Snape, who responds by reaching his hand towards hers, and finally, the hook-nosed man snaps back into reality, the surroundings reappearing and Harry replacing Lily's image once again. Snape slowly lowers his wand and stands solemnly in front of Harry. No words are needed.
Basically, the reminder of Lily is what will keep Snape sane and will force him to remember what things are worth fighting for.