This is definitely an interesting argument. I can see merit in both sides of it. Its definitely one of those things that will run and run. My opinion is is that I can understand emulator writers wanting to charge for their work, because work takes time, and strictly speaking, it is the time that they would be charging for. However, the reverse-engineering that has to go on to allow this to happen is, in many cases, illegal.
Reverse engineering, for those who dont know, is the process of taking someone elses work (usually compiled code or similar) and looking at it to try and work out what it does for the purposes of copying the concepts and process - all be it in a different way.
In reality, its one of those things that companies would probably (and almost always DO) turn a blind eye to when the end product is a homebrew or non-profit making product, unless the free availability of such product is going to infringe heavily on their business interests.
A parallel would be taking a well-known song, working out all the instrumental parts, getting a band together and recording it, then releasing it (free or not) without the original author's permnission. You are still negating the many hours it took to write and originally record that son, even if you ARE putting your time into figuring it out and learning it etc. In reality again, many bands play covers at gigs, which in reality arn't strictly legal without the record companys permission.
The main difference with emulated consoles/computers is the same argument brought up again and again with roms - that most of the time, the system/games are no longer a going business concern, so the companies are not that bothered. It is when the emulated system takes away from the business of a company, and even makes COPIES of it's games playable on a totally different system that the companies get pissed off. And I dont blame them. This is the main reason why I really DONT want a good GBA emulator on the GP32 - it could be its death knell.
A case in point is that of the Playstation emulator for the PC and Dreamcast - Bleem. That started out as freeware, but graduated into a very good, but charged-for product. I myself actually bought it just before Sony decided to sue the hell out of the company and shut it down.
Thing is, we all know that if Nintendo happened to do anything more than than fart in the general direction of Gamepark, they would probably send our favorite little Korean company to that place that so many other have gone and never returned from. Yes, I know that GP isn;t developing the emus themselves, but it's still something to think about.
What it boils down to is that, whatever you think of paying for emulators, if the authors decide to charge, they are strictly speaking charging for the research and development of another company. It's up to that company if they want to get pissed about it, but if they do, they're unlikely to lose an argument in court. It looks like, legally anyway, emulators will have to stay as donationware if the authors want to stay from being pulled through the courts.
Anyway - I'll stop now