One feature of the Twelve-Factor methodology is step two, explicitly declaring your dependencies. We've already touched on this, but it's worth reiterating and to seeing npm makes this easy to accomplish.
Step one of the Twelve-Factor methodology is ensuring that your application code is checked into a source code repository. You probably already know this, and even have the best of intentions to ensure that everything is checked in. With Node.js, each module should have its own repository rather than putting every single last piece of code in one repository.
Each module can then progress on its own timeline. A breakage in one module is easy to back out by changing the version dependency in ...