I think you guys (PGC) sort of misreported this one. It's still a BS patent, but it's more specific than you think. The patent reads, "A software emulator for emulating a handheld video game platform such as GAME BOY.RTM., GAME BOY COLOR.RTM. and/or GAME BOY ADVANCE.RTM. on a low-capability target platform (e.g., a seat-back display for airline or train use, a personal digital assistant, a cell phone) uses a number of features and optimizations to provide high quality graphics and sound that nearly duplicates the game playing experience on the native platform."
You'll notice it's referring to emulating ANY handheld game (this actually extends BEYOND Gameboy and into the realm of NGPC, Game Gear, etc.), but only on a "low-capability target platform (e.g., a seat-back display for airline or train use, a personal digital assistant, a cell phone)." So emulating handheld games on a "high-capability" platform (Gamecube, PC, etc.) would still be legal, although the "low-capability" definition is FAR too subjective and should never have been allowed through the patent process.
You'll also notice this patent was filed back in 2000, so while it conveniently applies to emulators on the Zodiac, it was good foresight on Nintendo's part, not hindsight, that allowed that to happen.