My favorite obscure WOTC D&D campaign setting would definately have to be Diablo II. (Diablo's Red Lightning attack ignores normal evasion, and treats improved evasion as regular evasion instead - nasty!)
Depending on how broadly you're defining "campaign setting" and "D&D", you may also want to include the various d20 Modern settings (or at least Urban Arcana), and if Spelljammer is making the list, then you're actually including content published by Paizo under license from WOTC.
And if Paizo content counts... well, you'll have to start working up a formal definition of what is and isn't D&D, because Spelljammer was published as a mini-setting in the Polyhedron mini-magazine in the back of Dungeon magazine in the early 2000s, and there were like ten mini-settings a year in that format, including a mecha system, three early precursors to d20 Modern, a sword-and-planet setting that I may have to track down, etc.
I believe WOTC also published the d20 Wheel Of Time RPG, and there was also an issue of Dragon (#307) that mostly was content for George R. R. Martin's "Song Of Ice And Fire" setting (Westeros).
Additionally, WOTC is no longer the publisher of the Dragonlance campaign setting books.
Finally, there two or three later issues of Dragon which consisted entirely of articles with bits of support for old campaign settings which were otherwise no longer supported - in some cases, for many years. Up to you if publishing content for a campaign setting counts as publishing the campaign setting.