That's a tough one. My favorite studio is Team Ico, so Ico and SoTC would certainly be up there.
As far as series go, I'd probably give the edge to Infamous or Wipeout. Uncharted has been mostly excellent and The Last of Us is outstanding, too (although I hope it doesn't become a series).
Killzone has been wildly inconsistent, unfortunately. Ratchet & Clank and God of War, conversely, have been consistently great. I adore the original Jak but it was downhill after that (although Daxter on PSP was a nice return to form). Folklore is a solid IP that didn't get enough love. And Gravity Rush has a lot of potential. Patapon and Sly Cooper deserve honorable mention as well.
Does Demon's Souls count? If so, that would be tops also.