The decision is up to a patent examiner at the USPTO. In theory they are supposed to research the origins of a patent to determine if there is any "prior art" that would make the idea obvious. A patent is supposed to be issued only if the idea is non-obvious. Given the length of time emoticons have been around, I can't see how MS could patent any manipulation of them. People have been moving emoticons back and forth between graphics and text for a long time, and that contsitutes prior art.
However, in reality, patent examiners are horribly overworked (largely due to frivolous crap like this) and will sometimes issue or reject patents based on very, very incomplete research. The end result is that patenting things has become way too much of a gambling game. Since it costs almost nothing to play and the rewards are potentially huge, companies will keep on swamping the PTO and hope that they can use the patents to extort their way to fame and riches.
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