There's a split up of the MySQL manuals to one for each version, including MySQL 4.1, 5.0 AND 5.1 (!).
They can be accessed at http://dev.mysql.com/doc/refman/4.1/en/index.html, http://dev.mysql.com/doc/refman/5.0/en/index.html and http://dev.mysql.com/doc/refman/5.1/en/index.html.
Very interesting is the Change History on MySQL 5.1 which you can find at http://dev.mysql.com/doc/refman/5.1/en/news.html. It seems, the release of the first 5.1 alpha version is not far ahead.