Populate() ref aninhado na matriz de objetos

Algum código, talvez, também algumas correções em sua abordagem. Você meio que quer um tipo de junção "manyToMany" que você pode fazer da seguinte forma:

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


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


var userSchema = new Schema({
  email: String,
  displayName: String,
  subscriptions: [{ type: Schema.Types.ObjectId, ref: 'UserShow' }]
});

userShows = new Schema({
  show: { type: Schema.Types.ObjectId, Ref: 'Show' },
  favorite: { type: Boolean, default: false }
});

var showSchema = new Schema({
  title: String,
  overview: String,
  subscribers: [{ type: Schema.Types.ObjectId, ref: 'User' }],
  episodes: [{
    title: String,
    firstAired: Date
  }]
});


var User = mongoose.model('User', userSchema);
var Show = mongoose.model('Show', showSchema);
var UserShow = mongoose.model('UserShow', userShows);

var user = new User({
  email: '[email protected]',
  displayName: 'bill'
});

user.save(function(err,user) {

  var show = new Show({
    title: "Some Show",
    overview: "A show about some stuff."
  });

  show.subscribers.push( user._id );
  show.save(function(err,show) {
    var userShow = new UserShow({ show: show._id });
    user.subscriptions.push( userShow._id );
    userShow.save(function(err,userShow) {
      user.save(function(err,user) {
        console.log( "done" );
        User.findOne({ displayName: "bill" })
          .populate("subscriptions").exec(function(err,user) {

          async.forEach(user.subscriptions,function(subscription,callback) {
              Show.populate(
                subscription,
                { path: "show" },
              function(err,output) {
                if (err) throw err;
                callback();
              });

          },function(err) {
            console.log( JSON.stringify( user, undefined, 4) );
          });


        });
      });
    });
  });

});

Isso deve mostrar uma resposta preenchida muito parecida com esta:

{
    "_id": "53a7b8e60462281231f2aa18",
    "email": "[email protected]",
    "displayName": "bill",
    "__v": 1,
    "subscriptions": [
        {
            "_id": "53a7b8e60462281231f2aa1a",
            "show": {
                "_id": "53a7b8e60462281231f2aa19",
                "title": "Some Show",
                "overview": "A show about some stuff.",
                "__v": 0,
                "episodes": [],
                "subscribers": [
                    "53a7b8e60462281231f2aa18"
                ]
            },
            "__v": 0,
            "favorite": false
        }
    ]
}

Ou sem o "manyToMany" também funciona. Observe aqui que não há nenhuma chamada inicial para preencher:

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


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


var userSchema = new Schema({
  email: String,
  displayName: String,
  subscriptions: [{
    show: {type: Schema.Types.ObjectId, ref: 'UserShow' },
    favorite: { type: Boolean, default: false }
  }]
});


var showSchema = new Schema({
  title: String,
  overview: String,
  subscribers: [{ type: Schema.Types.ObjectId, ref: 'User' }],
  episodes: [{
    title: String,
    firstAired: Date
  }]
});


var User = mongoose.model('User', userSchema);
var Show = mongoose.model('Show', showSchema);

var user = new User({
  email: '[email protected]',
  displayName: 'bill'
});

user.save(function(err,user) {

  var show = new Show({
    title: "Some Show",
    overview: "A show about some stuff."
  });

  show.subscribers.push( user._id );
  show.save(function(err,show) {
    user.subscriptions.push({ show: show._id });
    user.save(function(err,user) {
        console.log( "done" );
        User.findOne({ displayName: "bill" }).exec(function(err,user) {

          async.forEach(user.subscriptions,function(subscription,callback) {
              Show.populate(
                subscription,
                { path: "show" },
              function(err,output) {
                if (err) throw err;
                callback();
              });

          },function(err) {
            console.log( JSON.stringify( user, undefined, 4) );
          });


        });
    });
  });

});