A good solution hasn't been common. Try to use babel with gulp. You have to just glob a bunch of files and hope you've covered all your dependencies. It becomes a mess once you get into more complicated stuff.

Webpack also handles sourcemaps flawlessly, and you get tons of other stuff like http://webpack.github.io/docs/hot-module-replacement.html.

In my experience, this approach really shines when you are building an "isomorphic" app. When the same code is expected to run in the browser and on the server, having a build tool that knows about both your entire dependency graph and your different build targets is a huge boon.

For example, you get hashed filenames (for far-future cache expiration in the browser) for free (no manifests or runtime reconciliation of names to assets necessary).