I personally think eBoy was harmful to pixel art as a genre, because it was for years the supposed masterwork of pixel art, with its crappy technique, single-minded execution, etc. They basically sucked the oxygen out of the room for the rest of us for a good long while.
That said, it was an integral part of our history.
EDIT: I'd like to submit that Prince of Persia should make the list maybe. Its fluid animation style was a direct influence on many pixel art classics, such as Flashback. There's not a lot of animation stuff in the list right now and I think PoP was really influential.