Here's a JavaScript implementation of the Durstenfeld shuffle, an optimized version of Fisher-Yates:

/* Randomize array in-place using Durstenfeld shuffle algorithm */
function shuffleArray(array) {
    for (var i = array.length - 1; i > 0; i--) {
        var j = Math.floor(Math.random() * (i + 1));
        var temp = array[i];
        array[i] = array[j];
        array[j] = temp;
    }
}

It picks a random element for each original array element, and excludes it from the next draw, like picking randomly from a deck of cards.

This clever exclusion swaps the picked element with the current one, then picks the next random element from the remainder, looping backwards for optimal efficiency, ensuring the random pick is simplified (it can always start at 0).

Note the loop condition skips i==0, since j can only ever be 0 then, leading to no swap.

Algorithm runtime is O(n). Note that the shuffle is done in-place so if you don't want to modify the original array, first make a copy of it with .slice(0).

EDIT: Updating to ES6 / ECMAScript 2015

The new ES6 allows us to assign two variables at once. This is especially handy when we want to swap the values of two variables, as we can do it in one line of code. Here is a shorter form of the same function, using this feature.

function shuffleArray(array) {
    for (let i = array.length - 1; i > 0; i--) {
        const j = Math.floor(Math.random() * (i + 1));
        [array[i], array[j]] = [array[j], array[i]];
    }
}