Nintendo and Team Ninja. I think that would turn out well.

Sony + valve ps4 would be amazing. I'd also like to see team ninja work with sony santa monica on a new God of war. Creative assembly working with nintendo on advance wars/fire emblem would be crazy too.

1 more, GSC to make an open world killzone game

Nintendo and SquareEnix. (Moreover, The Pokemon Company and SquareEnix.)

Retro Studios and Valve to make Half-life 3 or Metroid Prime 4.
Great AI, Intelligent use of physics, innovative gameplay, state of the art level design and art direction.

Undead Labs + Rockstar North + Bethesda = fucking awesome Open world ZRPG

Square Enix + Nintendo = Kingdom Hearts but instead of Disney and bad gameplay design, you get Nintendo and hopefully get good gameplay design.

Naughty Dog + Retro = Any project, most likely will turn out to be one of the most highly looked upon projects

Sega + Rockstar = Could provide an interesting twist to the very great Yakuza series, however it could be for the worse.

Activision + EA = Could make the most evil project ever, but hey at least Activision will tell you the project is evil....EA side would make it look like the project is for gamers.

Atlus + Level 5 = Could make an awesome game together with a mix of variety and awesomeness.

Nintendo and Sega - I want to see a Mario and Sonic platformer. Enough of this meeting up at the Olympic games stuff.