a.js

function Hoge(name) {
  this.name = name;
}
Hoge.prototype.greet = function() {
  return 'Hello, ' + this.name;
};
Hoge.prototype.toJSON = function() {
  var key, ret = { __meta__ : {} };
  for (key in this) {
    switch (typeof(this[key])) {
      case 'string':
      case 'number':
      case 'boolean':
      case 'object':
        ret[key] = this[key];
        break;
      case 'function':
        ret.__meta__[key] = this[key].toString();
        break;
    }
  }
  return ret;
};

function deserialize(s) {
  var d = JSON.parse(s),
  f = function() {},
  meta = d.__meta__,
  k, proto = {};
  delete(d['__meta__']);

  for (k in meta) {
    proto[k] = Function('return ' + meta[k])();
  }
  f.prototype = proto;

  var ins = new f(),
  p;
  for (p in d) {
    ins[p] = d[p];
  }

  return ins;
}


var hoge = new Hoge('test');
var s = JSON.stringify(hoge);
var ins = deserialize(JSON.stringify(hoge));

console.log(ins.name);
console.log(ins.greet());