The doodle is self-referential because many people will think that the doodle itself is an unexplained phenomenon.
To make things more interesting, Google posted an encrypted message on its Twitter account:
1.12.12 25.15.21.18 15 1.18.5 2.5.12.15.14.7 20.15 21.19
decrypted as "All your O are belong to us", a reference to the popular Internet meme "All your base are belong to us".
The doodle's URL is http://www.google.com/logos/go_gle.gif, which suggests that there's a missing "O".
Some people suggest that the doodle could be connected to the Exeter UFO Festival. "The Exeter incident was a highly-publicized UFO sighting that occurred in September 1965, approximately 5 miles from Exeter, New Hampshire, in the neighboring community of Kensington."
Update: From what I understand from this post published by Google Korea's blog, this is the first from a series of doodles that provide clues to solve the mystery: who's celebrated by Google? The next doodle will be posted on September 15th and the hints are: mystery, invisible and novel. As someone suggested in the comments, Google probably celebrates the birthday of H. G. Wells, the author of "The Invisible Man" and "The War of the Worlds".
Update 2 (Sept. 15): There's a new doodle that points to a search for [crop circles] and this time there's a missing "l". Google posted on Twitter some coordinates: 51.327629, -0.5616088 that send you to this address: 1-7 Woodham Rd, Woking, Surrey GU21 4, UK. As you probably know, H. G. Wells was born in England. "H. G. Wells moved to Woking in 1895. This was the beginning of his writing career, and whilst living in the town he wrote several books including War of the Worlds," mentions wokingsurrey.com.
Update (Sept. 20): Indeed, Google's doodles were related to H. G. Wells' birthday. "Inspiration for innovation in technology and design can come from lots of places; we wanted to celebrate H.G. Wells as an author who encouraged fantastical thinking about what is possible, on this planet and beyond. And maybe have some fun while we were doing it," explains Google. Here's the third and final doodle:
