The one I know off the top of my head is Madhouse. They worked on stuff like Summer Wars, Ninja Scroll, the aforementioned One Punch Man, and of course one of my favorite animes, Hellsing Ultimate. They put a lot of effort into their work. This is especially amazing if what I heard about their budget was true.
Yeah, I don't know a lot of other animation studios. Maybe Gonzo. But for other animes I've seen, I can only associate them to a studio each, as I've only seen one of their works.