There's also Cave Story, which came out in 2004. I find it really impressive that the creator made the art, music, music editor, sound effect editor, music format, game engine, and stage editor, with only C++ and the Win32 interface, all while keeping a full time job (although he deliberately picked a low-key job at a printer company so he could work on Cave Story in his free time more). And halfway through, he got married and had kids, which slowed development.