If you are using meshes containing lots of vertices, I would advise you to use the openCTM webGL loader instead of zip hacking. Here is a link to the loader : http://threejs.org/examples/webgl_loader_ctm.html
This mesh compression tool uses LZMA compression method and can reduce the size of your files by 93%...
Concerning the JSONLoader, using an array might help:
var meshes = [];
...
var loader = new THREE.JSONLoader();
var onGeometry = function(geom)
{
var mesh = new THREE.SceneUtils.createMultiMaterialObject(geom, [material]);
meshes.push( mesh );
...
scene.add(mesh);
};
loader.load("yourfile.js", onGeometry);
Hope this helps