For me it is Alan Wake. The gameplay might bore after a while, but the story is always superb. Even in American Nightmare they can pull off a believable and deep plot with all the repetition. The guys at Remedy are amazing.
Runner-ups: Atlus with Shin Megami Tensei and (late) Cavia with Nier. Atlus makes interesting plots to me, that deal with more than bare justification for the gameplay, while Cavia was awesome with its realization of the universe from Nier, even if we probably won't see more of it.
p.s. - writting in a tablet is slow and frustrating. I hate it!