Copy all of the properties in the source objects over to the destination object, and return the destination object. This method will recursively copy mutual properties which are also objects.

underscore.mixin.deepExtend.coffee

# Create a deep copy of an object. - CoffeeScript conversion of @cederberg's deepClone implementation https://github.com/documentcloud/underscore/pull/595
deepClone = (obj) ->
	if !_.isObject(obj) or _.isFunction(obj) then return obj
	if _.isDate obj then return new Date do obj.getTime
	if _.isRegExp obj then return new RegExp obj.source, obj.toString().replace(/.*\//, "")
	
	isArr = _.isArray obj or _.isArguments obj
	
	func = (memo, value, key) ->
		if isArr then memo.push deepClone value
		else memo[key] = deepClone value
		return memo;
	return _.reduce obj, func, if isArr then [] else {}

# Is a given value a basic Object? i.e.: {} || new Object()
isBasicObject = (object) ->
	(object.prototype is {}.prototype or object.prototype is Object.prototype) and _.isObject(object) and not _.isArray(object) and not _.isFunction(object) and not _.isDate(object) and not _.isRegExp(object) and not _.isArguments(object)

# Returns a list of the names of every object in an object — that is to say, the name of every property of the object that is an object.
basicObjects = (object) ->
	_.filter _.keys(object), (key) -> isBasicObject object[key]

# Returns a list of the names of every array in an object — that is to say, the name of every property of the object that is an array.
arrays = (object) ->
	_.filter(_.keys(object), (key) -> _.isArray object[key])

# Copy and combine all of the properties in the source objects over to the destination object and return the destination object. This method will recursively copy shared properties which are also objects and combine arrays.
deepExtendCouple = (destination, source, maxDepth=20) ->
	if maxDepth <= 0
		console.warn '_.deepExtend(): Maximum depth of recursion hit.'
		return _.extend destination, source

	sharedObjectKeys = _.intersection(basicObjects(destination), basicObjects(source))
	recurse = (key) ->
		source[key] = deepExtendCouple destination[key], source[key], maxDepth-1

	recurse sharedObjectKey for sharedObjectKey in sharedObjectKeys

	sharedArrayKeys = _.intersection(arrays(destination), arrays(source))
	combine = (key) ->
		source[key] = _.union destination[key], source[key]
	
	combine sharedArrayKey for sharedArrayKey in sharedArrayKeys

	_.extend destination, source

# Copy and combine all of the properties in the supplied objects from right to left and return the combined object. This method will recursively copy shared properties which are also objects and combine arrays.
deepExtend = (objects..., maxDepth) ->
	if !_.isNumber maxDepth
		objects.push maxDepth
		maxDepth = 20
	
	if objects.length <= 1 then return objects[0]
	if maxDepth <= 0 then return _.extend.apply this, objects
	
	finalObj = do objects.shift
	while objects.length > 0
		finalObj = deepExtendCouple(finalObj, deepClone(do objects.shift), maxDepth)

	return finalObj

_.mixin
	deepClone: deepClone
	isBasicObject: isBasicObject
	basicObjects: basicObjects
	arrays: arrays
	deepExtend: deepExtend

underscore.mixin.deepExtend.example.coffee

foo =
	array: [3, 4, 5, 1, 'rawr', 'foo']
	name:
		first: "Earl"
		last: "Jones"
	job: "Winning"
	friends:
		"01234":
			name:
				first: "Whodat"

bar =
	array: [1, 2, 3, 'rawr', 'zoom']
	name:
		middle: "Samus"
	job: "Farmer"
	friends:
		"01234":
			name:
				last: "Mook"
			friends:
				deep:
					connection:
						going:
							all:
								the:
									combined: "Heyo!"
									way:
										down:
											depth: "Too Deep?"
											hear: "Not Too Deep"

blam =
	name:
		first: "Eddie"
	job: "Mugger"
	friends:
		"01234":
			name:
				first: "Honorary"
			friends:
				deep:
					connection:
						going:
							all:
								the:
									way:
										down:
											depth: "Way Too Deep!"
											see: "What I mean?"
		"43210":
			name:
				first: "Guy"
				last: "Rogers"

# Use deepClone when testing because deepExtend will modify the first parameter
console.log(_.deepClone(foo),_.deepClone(bar),_.deepClone(blam))
console.log('default', _.deepExtend(_.deepClone(foo), bar, blam))
console.log('0', _.deepExtend(_.deepClone(foo), bar, blam, 0))
console.log('20', _.deepExtend(_.deepClone(foo), bar, blam, 20))
console.log('mixed-default', _.deepExtend(_.deepClone(blam), foo, bar, 20))
console.log('mixed-0', _.deepExtend(_.deepClone(blam), foo, bar, 0))
console.log('mixed-20', _.deepExtend(_.deepClone(blam), foo, bar, 20))
console.log(foo,bar,blam)

underscore.mixin.deepExtend.js

(function() {
  var arrays, basicObjects, deepClone, deepExtend, deepExtendCouple, isBasicObject,
    __slice = [].slice;

  deepClone = function(obj) {
    var func, isArr;
    if (!_.isObject(obj) || _.isFunction(obj)) {
      return obj;
    }
    if (_.isDate(obj)) {
      return new Date(obj.getTime());
    }
    if (_.isRegExp(obj)) {
      return new RegExp(obj.source, obj.toString().replace(/.*\//, ""));
    }
    isArr = _.isArray(obj || _.isArguments(obj));
    func = function(memo, value, key) {
      if (isArr) {
        memo.push(deepClone(value));
      } else {
        memo[key] = deepClone(value);
      }
      return memo;
    };
    return _.reduce(obj, func, isArr ? [] : {});
  };

  isBasicObject = function(object) {
    return (object.prototype === {}.prototype || object.prototype === Object.prototype) && _.isObject(object) && !_.isArray(object) && !_.isFunction(object) && !_.isDate(object) && !_.isRegExp(object) && !_.isArguments(object);
  };

  basicObjects = function(object) {
    return _.filter(_.keys(object), function(key) {
      return isBasicObject(object[key]);
    });
  };

  arrays = function(object) {
    return _.filter(_.keys(object), function(key) {
      return _.isArray(object[key]);
    });
  };

  deepExtendCouple = function(destination, source, maxDepth) {
    var combine, recurse, sharedArrayKey, sharedArrayKeys, sharedObjectKey, sharedObjectKeys, _i, _j, _len, _len1;
    if (maxDepth == null) {
      maxDepth = 20;
    }
    if (maxDepth <= 0) {
      console.warn('_.deepExtend(): Maximum depth of recursion hit.');
      return _.extend(destination, source);
    }
    sharedObjectKeys = _.intersection(basicObjects(destination), basicObjects(source));
    recurse = function(key) {
      return source[key] = deepExtendCouple(destination[key], source[key], maxDepth - 1);
    };
    for (_i = 0, _len = sharedObjectKeys.length; _i < _len; _i++) {
      sharedObjectKey = sharedObjectKeys[_i];
      recurse(sharedObjectKey);
    }
    sharedArrayKeys = _.intersection(arrays(destination), arrays(source));
    combine = function(key) {
      return source[key] = _.union(destination[key], source[key]);
    };
    for (_j = 0, _len1 = sharedArrayKeys.length; _j < _len1; _j++) {
      sharedArrayKey = sharedArrayKeys[_j];
      combine(sharedArrayKey);
    }
    return _.extend(destination, source);
  };

  deepExtend = function() {
    var finalObj, maxDepth, objects, _i;
    objects = 2 <= arguments.length ? __slice.call(arguments, 0, _i = arguments.length - 1) : (_i = 0, []), maxDepth = arguments[_i++];
    if (!_.isNumber(maxDepth)) {
      objects.push(maxDepth);
      maxDepth = 20;
    }
    if (objects.length <= 1) {
      return objects[0];
    }
    if (maxDepth <= 0) {
      return _.extend.apply(this, objects);
    }
    finalObj = objects.shift();
    while (objects.length > 0) {
      finalObj = deepExtendCouple(finalObj, deepClone(objects.shift()), maxDepth);
    }
    return finalObj;
  };

  _.mixin({
    deepClone: deepClone,
    isBasicObject: isBasicObject,
    basicObjects: basicObjects,
    arrays: arrays,
    deepExtend: deepExtend
  });

}).call(this);

underscore.mixin.deepExtend.usage.js

var user = { "name": { "first": "Earl" }, "friends": ["0","1","3"], "job": "Mad Scientist", "pets": { "dog": "Ralph" } };
var userUpdate = { "name": { "last": "Duncan" }, "friends": ["6","9"], "job": "Happy Scientist", "pets": { "cat": "Judy" }, "city": "Portlandia" };

_.deepExtend(user, userUpdate);

// results in user equalling:
// { "name": { "first": "Earl", "last": "Duncan" }, "friends": ["0","1","3","6","9"], "job": "Happy Scientist", "pets": { "dog": "Ralph", "cat": "Judy" }, "city": "Portlandia" }

underscore.mixin.deepExtend.useCase.js

var user = { "name": { "first": "Earl" }, "friends": ["0","1","3"], "job": "Mad Scientist", "pets": { "dog": "Ralph" } };
var userUpdate = { "name": { "last": "Duncan" }, "friends": ["6","9"], "job": "Happy Scientist", "pets": { "cat": "Judy" }, "city": "Portlandia" };

_.extend(user, userUpdate);

// results in user equalling:
// { "name": { "last": "Duncan" }, "friends": ["6","9"], "job": "Happy Scientist", "pets": { "cat": "Judy" }, "city": "Portlandia" }

As dschi mentioned for the coffescript version, the js version should be
if (!_.isObject(obj) || _.isFunction(obj)) {
instead of
if (!_.isObject(obj || _.isFunction(obj))) {

What about this:

var clone = JSON.parse(JSON.stringify(obj));

Great catch @dschi and @senica, thanks!

@AndrewEastwood Nice deepClone replacement! You'll lose Date and RegEx handling, but if you're not using those data types that should work well.

@chrisritter Thanks for asking! License is WTFPL.
http://en.wikipedia.org/wiki/WTFPL

'null' values don't work. I get an error in isBasicObject:

TypeError: Cannot read property 'prototype' of null

The problem can be solved by switching the order of the first two clauses in the logical expression in isBasicObject().

  _.isObject(object) && (object.prototype === {}.prototype || object.prototype === Object.prototype)