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The json export plugin works well for simple geometries but it'll only export one mesh at a time - scenes and linked meshes aren't supported. For more complex things I export as Collada and use the colladaLoader that's in the examples in three.js's github repo.
This is also the best path if you have something with skinned animations.

Sadly, it's not without it's own problems. It has a few bugs that make it hard to import models from Maya or Autodesk's FBX to collada converter.

Also, the JSONLoader and file format used in this tutorial are almost deprecated.

Three.js has a newer JSON format[1], a new Blender exporter [2], and a new loader (THREE.ObjectLoader) in recent versions. They are much more fully featured and efficient compared to the earlier tools. They are more or less the preferred way to handle Blender->JSON->Three.js (at least for static meshes) now.

[1] https://github.com/mrdoob/three.js/wiki/JSON-Object-Scene-fo...

[2] https://github.com/mrdoob/three.js/tree/dev/utils/exporters/...

[3] https://github.com/mrdoob/three.js/blob/master/src/loaders/O...