Summary: Copyright is badly broken, out of touch with reality, and needs to be fixed.
When D&D third edition appeared, Wizards of the Coast provided a big chunk of the game material under the so-called Open Gaming License (OGL). This was a perpetual, unrevokable license that allowed people to create derived works. Essentially, Ryan Dancy was inspired by Free Software at the time and thought that this would help Wizards of the Coast to sell more core rulebooks. Let other people create adventures. 
At the same time, a second license was available to publishers: The d20 System Trademark License.  If publishers wanted to put the d20 logo on their product, they needed to get that license. That license was more restrictive than the OGL, and it could be terminated. In fact, when D&D fourth edition was announced, the d20 System Trademark License was revoked.
And now we’re getting to the main point of this post. Here is what Scott Rouse has said on the topic:
Unfortunately it appears that without the d20 System Trademark License you not only need to remove the logo but some other stuff as well – such as named references to the core books. This is a major hassle for small publishers that don’t expect a lot of sales on these products. Here’s what Matthew Sprange of Mongoose had to say on the topic:
It’s a neat idea. Unfortunately it remains a lot of work.
Some people thought that PDFs were here to stay, never go out of print, always be there for the last grognard to purchase. Except that with the d20 System Trademark License we’re now faced with a situation where this is no longer true. Essentially worthless PDFs have to be pulled from the infinte electronic bookshelves – no LongTail for you, mister! – because of the termination of this license.
Unlike books that are out of print, these PDF documents will not end up on AbeBooks and the Amazon Marketplace. There will be no legal second hand market because of legal issues. Even though I don’t remember any verbiage to that effect, if PDF documents are treated like software, there is no resale possible because you never “buy” software (you buy the medium it is printed on and the books), you “license” the software. And the license doesn’t allow you to make copies, to give it to anybody else, etc.
So, are PDF documents like physical books and can be resold?
If not, then massive “privateering” using peer to peer networks is going to be the only way to get these books. I want to be a privateer! 
Define external redirect: LongTail