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.
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.
