I think the eyes matter largely because of their effect on Snape- that's one of the reasons I believe Snape was in love with Lily. That love, which Dumbledore goes to great lengths on many occasions to indicate the power of, is what redeems him and makes him stronger than Voldemort. (It's the "old magic" Voldemort referred to in the graveyward in the movie). JK has a great deal of say in the movies, and I think all the odd looks Snape throws Harry is included for a reason, particularily when you think how many things they tossed out because of time constraints. I don't just look for clues in the books- I use the movies as well, primarily because she does have so much input into what makes it onscreen.
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