One practical scenario would be programmatically adding JQuery, custom JS and CSS file reference to your master page without modifying the master page it.
You need to create a Delegate Control and deploy it using a feature. Below is the snapshot for Feature.XML file.
<?xml version="1.0" encoding="utf-8"?>
Change the sequence number and control path and name as per your requirement.
In the MyCustomPageHead.ascx add the references of JS/CSS
<link rel="stylesheet" type="text/css" href="/_layouts/../../../jquery-ui-1.8.18.custom.css" />
Just deploy your feature and activate it in the site where you want to add JS and CSS references.