John Carmack - the guy behind the DOOM engine, Wolfenstein, Quake games, Commander Keen etc. If you are interested in this topic, Masters of Doom: How Two Guys Created an Empire and Transformed Pop Culture is a great read of what he and John Romero did.
Donald Knuth - alone wrote the TeX system back in the 1978. Also wrote the book The art of Computer Programming.
Bill Joy - wrote vi, csh, rlogin, rsh, and rcp.