Looks like npm-check-updates is the only way to make this happen now.

npm i -g npm-check-updates
ncu -u
npm install

On npm <3.11:

Simply change every dependency's version to *, then run npm update --save. ( Note: broken in recent (3.11) versions of npm).

Before:

"dependencies": {
    "express": "*",
    "mongodb": "*",
    "underscore": "*",
    "rjs": "*",
    "jade": "*",
    "async": "*"
  }

After:

"dependencies": {
    "express": "~3.2.0",
    "mongodb": "~1.2.14",
    "underscore": "~1.4.4",
    "rjs": "~2.10.0",
    "jade": "~0.29.0",
    "async": "~0.2.7"
  }

Of course, this is the blunt hammer of updating dependencies. It's fine if—as you said—the project is empty and nothing can break.

On the other hand, if you're working in a more mature project, you probably want to verify that there are no breaking changes in your dependencies before upgrading.

To see which modules are outdated, just run npm outdated. It will list any installed dependencies that have newer versions available.