Array of ObjectIds in Mongoose 3.8

Nothing wrong with the code you are listing so it's what you are not showing us that causes the problems.

When you reference you are going to both save a copy of the object in the collection and also add that related ObjectId value to the array of objects that are in "reply" in your case.

There are several ways to do it, but a good safe MongoDB way is using $push to add additional items.

As a complete example:

var async = require('async'),
    mongoose = require('mongoose'),
    Schema = mongoose.Schema;


var userSchema = new Schema({
  "name": String
});

var messageSchema = new Schema({
  "sender": { "type": Schema.Types.ObjectId, "ref": "User" },
  "replies": [{ "type": Schema.Types.ObjectId, "ref": "Message" }],
  "roomId": String,
  "sendTime": { "type": Date, "default": Date.now },
  "content": String,
  "parentId": Schema.Types.ObjectId
});

var Message = mongoose.model( "Message", messageSchema );
var User = mongoose.model( "User", userSchema );

mongoose.connect('mongodb://localhost/test');

async.waterfall(
  [
    // Clean up samples
    function(callback) {
      async.each(
        [User,Message],
        function(model,callback) {
          model.remove({},callback);
        },
        callback
      )
    },

    // Create user
    function(callback) {
      User.create({ "name": "Bill" },callback);
    },

    // Create a message
    function(user,callback) {
      Message.create({
        "sender": user._id,
        "roomId": "1",
        "content": "message"
      },function(err,message) {
        callback(err,user,message);
      });
    },

    // Create a reply
    function(user,message,callback) {
      Message.create({
        "sender": user._id,
        "roomId": "1",
        "content": "reply",
        "parentId": message._id
      },callback);
    },

    // Save that reply on the parent
    function(message,callback) {
      Message.findByIdAndUpdate(
        message.parentId,
        { "$push": { "replies": message._id } },
        function(err,message) {
          console.info( message );
          callback(err);
        }
      );
    },

    // List that
    function(callback) {
      Message.find({},function(err,messages) {
        if (err) callback(err);

        console.log(
          "All:\n%s",
          JSON.stringify( messages, undefined, 4 )
        );
        callback();
      });
    }

  ],
  function(err) {
    if (err) throw err;
    mongoose.disconnect();
  }
);

And the output:

{ _id: 54f3dff198a8c85306a2ef67,
  sender: 54f3dff198a8c85306a2ef66,
  roomId: '1',
  content: 'message',
  __v: 0,
  sendTime: Mon Mar 02 2015 14:58:41 GMT+1100 (AEDT),
  replies: [ 54f3dff198a8c85306a2ef68 ] }
All:
[
    {
        "_id": "54f3dff198a8c85306a2ef67",
        "sender": "54f3dff198a8c85306a2ef66",
        "roomId": "1",
        "content": "message",
        "__v": 0,
        "sendTime": "2015-03-02T03:58:41.387Z",
        "replies": [
            "54f3dff198a8c85306a2ef68"
        ]
    },
    {
        "_id": "54f3dff198a8c85306a2ef68",
        "sender": "54f3dff198a8c85306a2ef66",
        "roomId": "1",
        "content": "reply",
        "parentId": "54f3dff198a8c85306a2ef67",
        "__v": 0,
        "sendTime": "2015-03-02T03:58:41.393Z",
        "replies": []
    }
]

That way if you called .populate() on an message that has "replies" present, it will go back to the collection and retrieve the related data and make it appear that data was part of that item as well.

Please not that such magic does not happen "recursively" without your own intervention. It's just a basic helper, so if you want more then you still have to do the lifting yourself.