Why aren't my font colors / scripts / Flash / Java applets showing up in my Plone site?

By default, Plone employs an HTML-filtering system when it transforms Plone documents into marked-up web pages. Certain tags, such as <font> and other deprecated tags in HTML, are removed so that the generated page is closer to XHTML, which does not allow deprecated tags. Other tags such as <script> and <embed> are disabled because they present certain security issues.
While avoiding the use of these tags is certainly the preferred “Plone way of doing things”, this isn’t always an option. Certain tools such as the TinyMCE editor use <font> and other filtered tags, and won’t be displayed by default, forcing the user to change the filtering.
Instructions on changing tag filtering can be found at this Plone article. Look under the section labeled “Safe HTML”. Note that you must have Plone 2.1.2 or later in order to configure Safe HTML.