All modesty aside, I consider myself pretty familiar with intellectual property law. I didn't mean to become so well acquainted but having been sued over trademark and dealing with Apple, Microsoft, and going through the patent process have taught me what is what.
Unfortunately, most people on the Internet know very little on these issues. That doesn't seem to stop them from writing highly charged opinionated articles that make broad claims of intellectual property.
First off, forget what you think you know about IP law in theory. Theory and practice are two different things:
http://www.avault.com/developer/getarticle.asp?name=bwardell8
In real life, intellectual property protection goes as far as your money will take you. So forget the "Oh well Microsoft couldn't do anything about it because they'd be in the wrong on issue X, Y, Z." Wrong. If someone has money and you don't, they can grind you into the dust. You tick off a company and they can squash you like a bug no matter how righteous you think. And if you're a company, a bigger company can do the same to you.
That said, let's talk about the issue as it relates to skinning:
There are 3 issues that crop up:
1) Copyright violations
2) Trademark violations
3) Tradedress violations
1) Copyright violations are what are known as rips. People who aren't familiar with IP law think everything is a copyright violation. They're wrong. Copyright law is very specific. And it has a lot of gray areas. It has to do with taking someone elses material and using it without authorization and reproducing it. There is a lot of gray area on derivative works (hence where the lawyers come in). This is particularly true in digital art. If I take your wallpaper, apply tons of filters to it, and resubmit it, am I violating your copyright? It's a gray area that only the moderators of a given site or the court system can really decide, typically on a case by case basis.
Here at WinCustomize, we throw out copyright violations. Rips are copyright violations. You take someone's wallpaper and upload it here, that's a copyright violation and it's history. You take someone's skin and upload it here, same deal. You take someone's Hoverdesk theme and port it to Litestep without permission that's a copyright violation and it's gone.
The gray area comes up when you've made significant changes to it. Let's say you've taken a Kaleidoscope theme and ported it to WindowBlinds but doing so changed the actual graphics quite a bit but the final skin looks pretty much the same. Does that violate copyright? That's a harder case but it DOES violate trade dress which we'll talk about in a minute and we'd delete such a skin here. Having a gray copyright issue is one thing, add tradedress and that puts it over the top.
2) Trademark. This is where you take something that is designed to be associated with something else and use it for your own purposes.
There are two types of trademark issues:
a) Unauthorized use of trademark

Trademark violations.
You start up a fan site for Episode 2 and have Star Wars logo and other things on there from the movies and you hvae unauthorized use of trademark. Some companies work hard to enforce their trademark and stop fan sites. The X-box and Lord of the Ring skins here are unauthorized uses of trademark. We let skins like that here because they fall in the same category as fan websites.
Trademark violations are a different matter. That's where you're using someone else's trademark and re-defining it. This creates confusion which is why trademarks were created in the first place. If I took that X-box logo and used it to create "X-box Computers" which aren't affiliated with the game machine at all or are using it to sell a product designed to give users a false association then that can be a serious problem.
The two are quite similar and sometimes they decide that the former falls into the latter. Hence, if I start up a Coca-cola fan site they may be okay with that until I start selling Coca-Cola T-shirts. Then they may shut me down for giving a false association with their trademark.
3) Trade dress
This is fairly specific to skinning actually. When Apple demands people get rid of Aqua skins, they refer to Trade DRESS violations unless the skin actually uses the Aqua images and then they can bring in copyright violations as well (yes, icons ARE protected by copyright).
Tradedress is similar in enforcement to trademarks. Many many sites use the XP look. This is an unauthorized use of trade dress. The same is true of Luna skins. Microsoft is well aware of these and thus far has not objected.
So why do sits like Wincustomize allow OS skins? Aren't they rips? Nope. They do not violate copyright (unless they literally stole the bitmap resources which is possible but hard to tell). But they are unauthorized use of trade dress.
So when people argue that skin sites have double standards on ripping, the fact is, no, they don't.
Skins Sites police copyright violations. Rips are copyright violations. We find them, we eliminate them.
We trade the latter two issues (trade dress and trade mark) much like the equivalent of fan sites.
Geocities and Yahoo have zillions of Star Trek, Buffy the Vampire slayer, Star Wars, Lord of the Rings, etc. fan sites on them. There are fan sites for most popular games, etc. WinCustomize treats this in the same way as Geocities and Yahoo handle the fan sites they host - if the trade dress/trademark holder objects, we'll help them enforce their rights. Otherwise we'll work on the assumption that they're sane companies that want positive expressions by fans to exist.
I for one would love to see an Episode II theme. And I suspect if George Lucas were into skinning he'd want one too.