As far as first party goes, I'd have to say it's a tie between Bungie and Naughty Dog. While the partnership with Microsoft didn't last very long, the Halo franchise created tons of ground for the Xbox brand to stand on. Naughty Dog wasn't as important to Sony like how Bungie were to Microsoft but they contributed just as much to the Playstation brand when they've made 3 breakout IPs such as Crash Bandicoot, Uncharted, and The Last of Us ...
Overall I'd have to say Rockstar was the best acquistion since Grand Theft Auto was a persistent phenomenon ...
FYI, Rare wasn't acquired by Nintendo. They had a partnership in which Nintendo owned 49% of the stake. Anyways it was a smart idea to dump the rest of it to Microsoft when they turned to crap ...
