An update to a plugin was causing me problems so I did not want to update the plugin until a fix was released. To exclude the plugin (or a theme) from notifying that there is an update I performed the following (dirty) hack. Just remember to fix everything back when a fix is released!
I located the main plugin file under wp-content/plugins/pluginname/pluginname.php
The meta data about the plugin is at the top of the file and includes the Plugin Name, Description etc. I manually amended the Version number to something very high i.e. from 1.12 to 4.1.2
So when WordPress checks for updates it thinks that I have a much later version of the plugin than is available on the WordPress Plugin Directory, and does not notify that there is an update available. This solves my issue in the short-term but beware of the security issues of not updating.
Plugin Name: MegaPlugger Plugin URI: http://somewebsite.com/megaplugger Description: Easily create mega stuff on your site. Requires PHP5 and WP3.5 Version: 4.1.2 Author: J Schmoe Author URI: http://somewebsite.com