Difference between revision 5 and current revision
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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 In fact, when D&D fourth edition was announced, the d20 System Trademark License was revoked.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:
The license ends in June 2008 so publishers will stop using it at that point. There will be a sell off period through the end of 2008 for publishers with stock in their warehouses. Product that is sold and sitting in a store or distributor is considered sold and fine. There will be no recall of product sitting in the channel. The major downside is for publishers who have so much stock they can’t move it in six months. For those who that is the case I suspect they have larger problems. PDF sellers will be asked to update their products within that six month time and remove the logo. 
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:
We produced a great deal of OGC under D20. Most of these books are now out of print, with just PDF copies available - by the end of the year these will disappear too, as it is not realistic for us to remove D20 licensing off every product we produced over the years. Just too many!
However, it seems a shame to have all this material simply disappear, so. . .
If there is any interest, we would be prepared to make the vast majority of our D20-based content available freely. In the past, there has been talk about an OGC Wiki of sorts, and I think we can kick such a project off in a sizeable way.
If a volunteer (or volunteers - you might have to be some sort of maniac to go through all this material solo!) were to come forward and create a suitable web site, we would happily supply electronic versions of our D20 lines for translation of OGC to such a web site. We would be very free with the material permissable, allowing you to effectively cut and paste large chunks of ‘fluff’ text alongside the OGC. 
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!