It appears like Nintendo is a perpetual victim when it comes to emulator software and piracy. Every week or so, there's a report of a new emulator or game remake in which people try to play a Nintendo game without paying for it. We don't hear about this often with Playstation or Xbox games despite some games being wanted forever (e.g. Mega Man Legends which finally did release). In one sense, it ticks me off because Nintendo is still selling the software and is one of the selling points of its hardware. Not only are they selling it, they are putting money into the software (even Quality Assurance costs money).
Sure that gets into the debate about what rights do we have when it comes to games we own. One problem is that people always use that software for games they don't own, and once they play it, they won't go out to buy it. Now one valid question is, "How is this different than renting or borrowing from a friend?" The quick answer is that it the other two still encourage purchasing the game in the end. Perhaps that will be a topic for another time. The other part is that to pirate games is to feed your own ego and selfishness. If you have to have it so bad, then go and buy it even at the excessively high prices on ebay.
So my idea is that Nintendo starts licensing the emulators. This way, when one comes out, they can justifiably claim that it is lost profits (to be fair, emulating their code is already a violation of their rights). However, the license will cost a certain amount based off the library it can play and the average price of such a game if Nintendo would put it on the eshop. That would mean the NES emulator alone would cost quite a bit. However, it has to be high so that the developers of the emulators pay to make up for the thousands of downloads they encourage.