Making character encoding work well on the web can be a bit of a tricky task. There are many different layers to get right, and many different places in which things can go wrong.
At Ephox we have seen many of our clients experience problems with character encoding, and different fonts. We've actually created a variety of different articles to help people make there content editing environment work better:
More recently I have been seeing some issues with encoding without EditLive! included. Sun proved to have a decent article talking about Character Conversions: http://java.sun.com/developer/technicalArticles/Intl/HTTPCharset/. This articles includes good details on how to setup your JSP/Servlet layers to support encodings well.
This proved to be the answer to my problems, and well worth viewing if you are having encoding related problems in a Java Web application.