Web Part and WCM scenario
You need to modify the ToolsFile.xml which is located in the following folder:
/Program Files/Common Files/Microsoft Shared/web server extensions/wpresources/RadEditorSharePoint/6.x.x.0__1f131a624888eeed/Resources/
and add the following tools:
<tool name="FlashManager" /><tool name="MediaManager" />
in the WCM scenario you will also need to add / set the AllowSpecialTags property to true. You can set it in the current page using SharePoint Designer. Click here for more information
SharePoint forms scenario (Lists, Blogs, etc.)
You cannot enter Media / Flash files in such scenarios. There RadEditor does not have control over the presentation view which means that we cannot control the output when it is not in edit mode.