In September, a stork was captured and put in jail under suspicion of being a spy. The bird had a wildlife tracker on it, and given our present-day situation with drones and shit, I can understand not wanting to deal with the treat of being surveiled by storks. The stork was released eventually, and then found "dead on an island in the Nile River, osuth of the ancient city of Aswan." Which in a way makes it sound more legitimately like espionage, not less. Admittedly, Egypt has been having a pretty rough time of late, what with the revolution and all. And then the disappointing new leader and then.....well, that's where I lost the trail of breadcrumbs. I'm ashamed to admit I don't know what subsequently happened in Egypt (other than the former president telling the court he did not acknowledge its authority to try him), but in the interest of honesty with y'all, I did not Google it so I could pretend.
I do understand that nobody in Egypt thought the stork itself was a spy, but rather just a vehicle for spying technology (and Shortlist.com has a list of animals accused of espionage, and this is a list of the top 10 Animals spies). Animals, especially birds, are used for things like message carrying all the time. Something drone-like would perhaps have been the logical next step (and still might who knows), and in 2011 a vulture was arrested in Saudi Arabia for the same thing (that story and others discussed a bit here on this Huffington Post article. Smithsonian had an article back in October about the CIA's animal spies.
According to this article, 250,000 pigeons were used to carry messages between Europe and Britain in WWII, with messages sometimes (often? always) in cipher. That article is in fact about a cipher whose key is no longer in anybody's possession, and somebody claiming to have cracked it anyway. The Germans also used carrier/"spy" pigeons, and the British had peregrine falcons for counter espionage. Apparently in 2008, Iran thought that it found a pair of spy pigeons, and this Wired article discusses the logistics of making such a thing happen, and this Mental Floss article talks about homing pigeons. In the interest of protecting against spy pigeons, And really, that's just talking about pigeons doing what they do, which is going home. B.F. Skinner, also in World War II, worked on "Project Pigeon", which was intended to be a pigeon guided missile system. The project was actually successful (operant conditioning for the win!) but due to a lack of respect and thus subsequent funding, it ended up being tabled.