I have a site where users can post stuff (as in forums, comments, etc) using a customised implementation of TinyMCE. A lot of them like to copy & paste from Word, which
HTML Purifier will create standards compliant markup and filter out many possible attacks (such as XSS).
For faster cleanups that don't require XSS filtering, I use the PECL extension Tidy which is a binding for the Tidy HTML utility.
If those don't help you, I suggest you switch to FCKEditor which has this feature built-in.