I hadn't considered the relationship between GPL and patents. I'll have to read more. Off the top of my head, I don't understand how anyone who went to the time and expense of getting a patent could ever jeopardize it with a GPLv3 release, since there's no bright line between a version of your program and a completely separate program that merely links enough code in to get a free patent license.
GPLv3 and Apache 2.0 are the two most widely used licenses which specifically mention patents. The goal of GPLv3 is (quoting from the license) to "[assure] that patents cannot be used to render the program non-free."
The "bright line" isn't always so bright. Consider if a hardware company pays MPEG LA for an MPEG license in order to sell a piece of video hardware based on Linux. The hardware company didn't get the patent, so while they must release the OS source under the GPL, they don't have the right to sublicense.
