Blizzard + Bioware for a Mass Effect MMO that captures the amazing narrative strengths of Bioware with the excellent MMO design of Blizzard. This would be the MMO that would actually pull me away from WoW, if it existed. I would also gleefully accept the reverse, Bioware taking the Warcraft narrative and making an awesome single player RPG for it (please please PLEASE give a Paragon interrupt where I can punch Garrosh in the face, I'll give you all my shiny purples...)
Nintendo + Square Enix since they seem to work extremely well together, enhancing each other's strengths and compensating for their weaknesses. Super Mario RPG 2, anyone?
Bioware + Square Enix for bringing a more interactive element to the Final Fantasy narrative (a real sequel to FF7 would make me happy, as long as it neglected most of the Complica... I mean, Compilation). And Bioware would start getting better (or more varied) character design for hot male love interests... less short hair and stubble, more long hair and elegant bishonen features, please. ^_^
Blizzard + Ubisoft (Montreal Studios) for Assassin's Creed: Dalaran. ;-)
Nintendo + Blizzard for designing a strong online multiplayer for some of Nintendo's classic franchises (either map/server based or a persistent world, MMO, whatever - imagine a game like Super Mario Galaxy where other people might be after the same star, racing for it, etc)
Ubisoft + Bioware for a more free-roaming take on the Mass Effect universe... an AC: Citadel kind of thing would be awesome.
Really, when in doubt I just tend to add Bioware (for the story design) or Blizzard (for MMO conversion). ;-)