Microsoft produces a lot of paper in a very large set of fields related to computer science. They invest a lot in research and I know it doesn't seem like it for those outside of academia. Hell I bet Bell labs didn't seem too impressive except for the transistor to the outside world.

Someone mentioned Haskell, they also do a lot in artificial intelligence, operating system research, security (yeah yeah I know), human computer interaction etc.

Not to long ago Apple passed Microsoft in profits, but that difference is much smaller than the difference in R&D budget. If you take that into account, Microsoft is much more profitable.