Are you trying to use the Media icon in TinyMCE?  I had the same issue: http://our.umbraco.org/forum/ourumb-dev-forum/bugs/25271-Media-generated-markup-in-TinyMCE-stripped-(471)

Now, I made some modifications to the tinyMceConfig.config to relax it a bit:

  <customConfig>
    <config key="entity_encoding">raw</config>
    <config key="spellchecker_rpc_url">GoogleSpellChecker.ashx</config>
    <config key="fix_content_duplication">false</config>
    <config key="extended_valid_elements">iframe[src|style|width|height|scrolling|marginwidth|marginheight|frameborder],figure,figcaption</config>
    <config key="apply_source_formatting">true</config>
    <config key="convert_fonts_to_spans">true</config>
    <config key="convert_newlines_to_brs">false</config>
    <config key="fix_list_elements">true</config>
    <config key="fix_table_elements">true</config>
    <config key="fix_nesting">false</config>    
  </customConfig>

If it still doesn't work, I'd go the jQuery route and hijax an anchor tag.  I did that for a Joomla site as a workaround to get external content served up in the site's template. This appears to be a simple solution: http://viget.com/inspire/youtube-chromeless-video-jquery-plugin  I would have a style defined as .video-link (Call it YouTube Link or something) so it's available in the dropdown and make the definition some kind of outline (like a macro) to indicate this will become a video.

It works if I use the old embed object code.  If I use the iframe version, now I get nothing as when I save/publish the iframe is stripped out.

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