The wp_footer() function is often used by plugins to insert PHP codes after everything else on your page. According to WordPress.org theme development documentation, you should place the wp_footer() function in the footer, which would be in the footer.php file.

One detail that WordPress.org doesn’t mention is that most plugins (i.e: Spam Karma 2, PodPress, and FireStats), using the wp_footer() function, tend to break your theme. A well-designed and well-built theme is nothing without a safely placed wp_footer() function.

Here’s my advice. Don’t place the wp_footer() function right before the end; that’s usually the closing body tag. Instead, place that function within a DIV or container. For example:

<div id=”container”>

Posts

Sidebar

<?php wp_footer(); ?></div>

If you do that, no matter what a certain plugin does to the footer of your theme, it doesn’t expand beyond the container or DIV containing the wp_footer() function. You can open up the footer.php file of the Greed theme for an example.Update:
Place the wp_footer() function within a style-less container (usually the outermost div with no backgrounds and images) that your layout doesn’t depend on. Otherwise, you might end up with an incomplete layout while waiting for a slow loading plugin.