shuffle.js

/* Shuffle
 Modified Fisher-Yates shuffle ( original from http://bost.ocks.org/mike/shuffle/ )
 to allow not shuffling specifically mapped array elements

 Example:
  var arry = [ 'aardvark', 'bison', 'cheeta', 'dingo', 'elephant', 'fawn', 'giraffe', 'hippo' ],
  // don't shuffle 'bison' or 'elephant'
      map  = [ '',         false,   '',       '',      false ];

  shuffle( arry, map ); // ["fawn", "bison", "dingo", "giraffe", "elephant", "hippo", "cheeta", "aardvark"]
  shuffle( arry, map ); // ["aardvark", "bison", "hippo", "dingo", "elephant", "cheeta", "giraffe", "fawn"]
  shuffle( arry, map ); // ["giraffe", "bison", "hippo", "dingo", "elephant", "aardvark", "fawn", "cheeta"]
  shuffle( arry, map ); // ["aardvark", "bison", "cheeta", "giraffe", "elephant", "fawn", "dingo", "hippo"]
*/
shuffle = function (array, map) {
	var swap, random,
	index = array.length;
	// While there remain elements to shuffle...
	while (index > 0) {
		// Pick a remaining element...
		random = Math.floor(Math.random() * index);
		if (map[index - 1] === false) {
			index--;
		}
		// skip elements that are mapped to false
		if (map[index - 1] !== false && map[random] !== false) {
			// And swap it with the current element
			index--;
			swap = array[index];
			array[index] = array[random];
			array[random] = swap;
		}
	}
	return array;
};

Demo: http://jsfiddle.net/Mottie/rU3mq/