I feel a deep sense of happiness when I use Google products like gmail and chrome. Every now and then they update the applications and things just work. They make things look so simple but they must be super complex in the back. That's great software.
Great software can only be built by great teams. That means everyone from engineers to managers. Give enough freedom to the team to execute. Treat them like people. Understand software.
No software methodology can save you. Let the team define its processes. Let common sense prevail. And then greatness will follow.