For keyboard and mouse vs. a controller, the keyboard and mouse win for me. For fps games, it is much easier to aim with the mouse and movement and other thins like that are more easily done. A good PC gamer will most likely beat a good console player on an fps if they have comparable skill and experience in the game.
For rts games, it really is a silly question as to who has the advantage. The lack of hotkeys and the ability to micro most of your units much more effectively and give better macro control definitely let's the PC dominate this genre.
Picture made by Aametherar the orc (Elves are the best!)