Weren't there also some individual licenses during 3e? I seem to remember Kenzer Co having a license to do Kingdoms of Kalamar as an officially licensed setting. You also had things like Dragonlance and Ravonloft licensed out to third parties to develop.
The "Kingdoms of Kalamar" license was actually a bit different from the other two, for legal reasons.
It all goes back to the "Dragon Archive" CDs, which included "Knights of the Dinner Table" strips for which Kenzer held the copyright. WotC had done the archive on the assumption that these were 'reprints', and so should be fine; Kenzer thought otherwise, and filed suit.
Ultimately, they agreed to a settlement, whereby Kenzer gained a license to publish KoK as an 'official' setting (including the use of the D&D logo), and also the rights to do... something with the old materials/adventures for the Hackmaster game.
(IIRC, a similar case did eventually go to judgement, and it was ruled that treating an archive as reprints was, indeed, fine. But, of course, the settlement was agreed by then, so that's a largely-irrelevant detail.)
So that's why the KoK books had the "Dungeons & Dragons" logo on the front cover, where Dragonlance and Ravenloft did not. It's also why there has never been a "Dungeon Archive" or a "Dragon Archive II".