The function register_deactivation_hook (introduced in WordPress 2.0) registers a plugin function to be run when the plugin is deactivated.
When a plugin is activated, the action 'deactivate_PLUGINNAME' hook is called. In the name of this hook, PLUGINNAME is replaced with the name of the plugin, including the optional subdirectory. For example, when the plugin is located in wp-content/plugin/sampleplugin/sample.php, then the name of this hook will become 'activate_sampleplugin/sample.php'. When the plugin consists of only one file and is (as by default) located at wp-content/plugin/sample.php the name of this hook will be 'activate_sample.php'.
This function is a wrapper for the 'deactivate_PLUGINNAME' action, and is easier to use.
<?php register_deactivation_hook($file, $function); ?>
If you have a function called myplugin_deactivate() in the main plugin file at either
use this code:
register_deactivation_hook( __FILE__, 'myplugin_deactivate' );
This will call the myplugin_deactivate() function on deactivation of the plugin.
A good example for a basic activation/deactivation/uninstall class by "kaiser" can be found here on WPSE: http://wordpress.stackexchange.com/questions/25910/uninstall-a-plugin-method-typical-features-how-to/25979#25979