How can I stop a plugin being updated?

Go into the PHP file for the plugin and change the information in the header comment. For example, this is the one from the Hello Dolly plugin that comes with WordPress:

/**
 * @package Hello_Dolly
 * @version 1.6
 */
/*
Plugin Name: Hello Dolly
Plugin URI: http://wordpress.org/plugins/hello-dolly/
Description: This is not just a plugin, it symbolizes the hope and enthusiasm of an entire generation summed up in two words sung most famously by Louis Armstrong: Hello, Dolly. When activated you will randomly see a lyric from <cite>Hello, Dolly</cite> in the upper right of your admin screen on every page.
Author: Matt Mullenweg
Version: 1.6
Author URI: http://ma.tt/
*/

Change the information in here to reflect that it is a “new” plugin. Just make sure you keep any copyright notices and such intact.