cogadh: Absolutely wrong, emulators are not illegal.
keeveek: Yes they are. Most of them are using modified console BIOS which is copyright violation. You think how they are emulating the console? Using it's modified engine. Which is a violation. (I am 100% sure PSX and PS2 emulators use SONY's BIOS for emulation, don't know exactly how things are for nintendo)
You clearly are very ill-informed about this subject or more likely have been subjected to a significant amount of FUD that you actually believe. No emulator uses a modified console BIOS, all of them that need the BIOS either require you to extract the BIOS from your own console, or, as in the case of PCSX, they have their own cleanly developed and perfectly legal custom BIOS. You can of course obtain the BIOS through less than legal means (torrents and the like), but that does not make the emulator itself illegal, just the act of obtaining the BIOS via that method illegal.
With Nintendo consoles at least up to the Nintendo 64 (including handhelds), there is no BIOS, they were purely hardware consoles, so all an emulator has to do is emulate the hardware environment. From the GameCube forward, I'm not sure what is required for emulation, I've never actually messed with GC or Wii emulators.
EDIT - whoops, there's a page two to this thread and all this was already covered. So let me add something new:
Regardless of the legality of emulators or the required components of emulators, we are talking about GOG selling Nintendo games here. If that were ever to happen (and that is a VERY big "if"), the games would be packaged along with the appropriate legal and approved by Nintendo emulator, similar to what GOG already does with DOSBox games and what Steam does with the Sega Classics console games it sells. Even if emulators were illegal, it is obviously not illegal for the rights holders of the games to choose to distribute those games with their own emulator.