Scripts removed on saving

Check that the Editor Profile Parameters allow the required tags

You can skip this step if you do not wish to allow script, style or php tags but still need to allow onmouseover / onmouseout tags.

In the JCE Control Panel, click on the Editor Profiles button.

Click on the Profile name that the user, usergroup or component is assigned to, eg: 'Default'

Click on the Editor Parameters tab, then on the Options tab.

Check that the Allow Javascript or Allow CSS or Allow PHP options are set to Yes (depending on which code type you need to insert).

Configure Joomla! Article filters

By default Joomla!  'cleans' content on saving, removing script tags, event attributes (such as onclick, onmouseover etc.) and style tags.

A simple article parameter change is all that is required to fix this.

Joomla! 1.5

See this article - http://docs.joomla.org/Why_does_some_HTML_get_removed_from_articles_in_version_1.5.8%3F 

Joomla! 1.7

1. In the Joomla! Article Manager, click on the Options button
2. In the Options Dialog, click on the Text Filters tab.
3. For the Super Users group, or any other trusted user group, set Filter Type to No Filtering. Make sure that you only set this option for user groups that can be trusted as setting the Filter Type to No Filtering will essentially allow the user to include any html in an article. 

Joomla! 2.5

1. In the Joomla! Global Configuration, click on the Text Filters tab.
2. For the Super Users group, or any other trusted user group, set Filter Type to No Filtering. Make sure that you only set this option for user groups that can be trusted as setting the Filter Type to No Filtering will essentially allow the user to include any html in an article.