You can add JavaScript and CSS files to your master page if you want to overwrite some default styles or add some functionality via a new script.
When you can't use a JavaScript or CSS concatenater, this method can be useful for adding scripts and styles to your site on the fly.
The standard ready function doesn't always work in WordPress plugins. Here's a workaround.
Here's a cool trick to run JavaScript on SharePoint 2010 wiki pages without editing the master page.