Sun recently said they would patent their 3D interface to protect them. They relased the code with the GPL license, which is supposed to be the most politically correct OSS license. So putting a patent on a GPL code is kinda strange.
But that's a really week argument when you think about it for a second ! Why would you need to patent something to protect you ? Prior art exists and means that if you can prove that you have made a system using the same technique as a patent, before the patent was applied, this patent is void. How could someone attack Sun for a system that is not patented yet and that they have made public ?! That's simply impossible...
So don't believe Sun or anyone else when they tell you that it's just to protect them !
(the only worth protection needed is to find if patents exist on the subject before you release something, only companies can afford that)