I'm currently using System JS with System JS Builder to bundle up my application, its assets, and the libraries that it references. My problem is that I can bundle libraries that are referenced explicitly in the index.html, e.g:
<script src="node_modules/es6-shim/es6-shim.min.js"></script>
<script src="node_modules/zone.js/dist/zone.js"></script>
<script src="node_modules/reflect-metadata/Reflect.js"></script>
<script src="node_modules/systemjs/dist/system.src.js"></script>
However, I can't figure out how I can bundle Angular 2 itself, or at least the modules required from Angular 2, as they aren't actually referenced in the HTML. How can this be done?
You can use a bundler like Webpack or Rollup (my preference because it does tree-shaking).
The Angular team appears to be putting together some great tooling around Rollup in time for the full release. The day 2 keynote of ng-conf this year discussed and demonstrated the offline compiler. Start watching this at 25:30.
Using systemjs-builder you can bundle Angular 2 with your app code and bundle your other libraries separately.
I bundled any library I would reference directly in HTML into a vendors.min.js, and any library referenced through my system.config.js plus app code into an app.min.js. In this example you can see that all the dependencies in Tour of Heroes are loaded into the page in <10 network requests (source code).