Outside of standard web functionality, the useful native app fuctionality can be found in cordova plugins:
https://cordova.apache.org/plugins/
Ways to pull a plugin into your app on PhoneGap Build:
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From npm:
<plugin name="phonegap-plugin-push" source="npm" />
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From a git repo:
<plugin spec="https://github.com/phonegap/phonegap-plugin-push.git#1.6.3" source="git" />
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PhoneGap Build's hosted repository: With the above two options, including private repositories, this repository can no longer be submitted to, and should no longer be used. For reference anyways:
<plugin name="com.phonegap.plugins.barcodescanner" source="pgb" />
See the individual plugins' documentation for it's usage and Javascript API.