Advantages of createElement over innerHTML?

There are several advantages to using createElement instead of modifying innerHTML (as opposed to just throwing away what’s already there and replacing it) besides safety, like Pekka already mentioned:

Preserves existing references to DOM elements when appending elements

When you append to (or otherwise modify) innerHTML, all the DOM nodes inside that element have to be re-parsed and recreated. If you saved any references to nodes, they will be essentially useless, because they aren’t the ones that show up anymore.

Preserves event handlers attached to any DOM elements

This is really just a special case (although common) of the last one. Setting innerHTML will not automatically reattach event handlers to the new elements it creates, so you would have to keep track of them yourself and add them manually. Event delegation can eliminate this problem in some cases.

Could be simpler/faster in some cases

If you are doing lots of additions, you definitely don’t want to keep resetting innerHTML because, although faster for simple changes, repeatedly re-parsing and creating elements would be slower. The way to get around that is to build up the HTML in a string and set innerHTML once when you are done. Depending on the situation, the string manipulation could be slower than just creating elements and appending them.

Additionally, the string manipulation code may be more complicated (especially if you want it to be safe).

Here’s a function I use sometimes that make it more convenient to use createElement.

function isArray(a) {
    return Object.prototype.toString.call(a) === "[object Array]";
}

function make(desc) {
    if (!isArray(desc)) {
        return make.call(this, Array.prototype.slice.call(arguments));
    }

    var name = desc[0];
    var attributes = desc[1];

    var el = document.createElement(name);

    var start = 1;
    if (typeof attributes === "object" && attributes !== null && !isArray(attributes)) {
        for (var attr in attributes) {
            el[attr] = attributes[attr];
        }
        start = 2;
    }

    for (var i = start; i < desc.length; i++) {
        if (isArray(desc[i])) {
            el.appendChild(make(desc[i]));
        }
        else {
            el.appendChild(document.createTextNode(desc[i]));
        }
    }

    return el;
}

If you call it like this:

make(["p", "Here is a ", ["a", { href:"http://www.google.com/" }, "link"], "."]);

you get the equivalent of this HTML:

<p>Here is a <a href="http://www.google.com/">link</a>.</p>