This Wikipedia article makes me think Take No Prisoners publishing rights might be at Ubisoft. "Heretic 2, Hexen 2's expansion, SoF and Singularity are owned by Activision."
What makes you say this about Heretic 2 and Hexen 2's expansion? Also aren't you forgetting Soldier of Fortune magazine in the SoF case?
"Heretic, Hexen, Deathkings and Hexen 2 are owned by Zenimax."
Technically by id Software, but they are in turn owned by Zenimax so the ultimate decision makers are the same. But this MIGHT make a difference in so far as intermediate decision makers are concerned and interal politics at Zenimax.
"Also Wolfenstein 2009 is nowhere to be seen, so I suspect Zenimax and Activision are talking about that one. "
The Wolfenstein franchise belongs to id Software(hence ultimately under the control of Zenimax as you correctly note), in fact id Software LLC just filed some new Wolfenstein related trademark applications(likely in connection with the new Wolfenstein game, Wolfenstein: New Order in development at Machinegames. However Activision published Wolfenstein 2009.
There is no specific reason to think that anyone else has those publishing rights. Unlike what some think(not accusing you of this misunderstanding, but I have seen it on the net) publishing rights don't automatically come along for ride so to speak when a development studio gets bought.
Publishing rights already signed away, need to be bought back in seperately negotiated deals between the acquiring company and those publishers, like Zenimax did with EA in the case of Rage. The Rage franchise never belonged to EA, id owned it so Zenimax got it as part of the deal when they acquired id. However the publishing rights were EA's. If Zenimax had wanted to they could have carried on the with the id-EA partnership. Such things happen all the time. However they opted to negotiate a buy back of the publishing rights with EA.
Similarly they ended up with the publishing rights for Quake 4 for Steam and Xbox 360(XBLA?). But I believe that may have been related to some contract expiration thing. Some like that happened with some XBLA/PSN game in an id franchise recently too.
So sure they may be interested in such a deal with Activision concerning Wolfenstein 2009 too, but until there any indications of anything else, we must assume that Activision Publishing Inc(a wholly owned subsidiary of Activision-Blizzard Inc) is the publisher of Wolfenstein 2009.
Publishing agreements are
complicated things. As are
Asset Purchase Agreements.