A fairly well known example is the evolution of the eyeball.
http://en.wikipedia.org/wiki/Evolution_of_the_eye
The eyes of squids and octopuses don't have a blind spot like vertebrates do, because the nerve endings are on the rear side of the retina. Which makes complete sense, and which begs the question why this feature hasn't been incorporated in vertebrates.
I'd expect that an expert could name many more examples on the top of his head. These two just happen to be examples that are easily understood by laymen.
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