Certainly, IMO, there were other, 'stronger' scenes (from a 'directorial' standpoint) within Cars that Pixar could have submitted, instead.
But that "soda moment" sequence from OTH would have been tough to beat. It really was one of the most memorable sequences, from any feature, last year. Not to mention, the funniest! .. the audience I saw it with literally had people falling out of their seats, laughing, during that scene.

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As for effects, yes, Cars was very deserving, but so were the other nominees. Here again, pertinent submitted clips from the films were viewed immediately before voting, so that they would be fresh in the voters' minds. I recall being particularly impressed with the 'effects' clips submitted for Flushed Away.