Normally, if you are beginning to use MySQL for the first time, or have no other reason to choose a specific version, we recommend going with version 4.1 for new databases, which is the default MySQL install from the Hosting Control Panel.
A brief rundown of the MySQL versions currently in use are:
MySQL 5.0: This is the current stable release. New releases are issued for bugfixes only; no new features are being added that could affect stability.
MySQL 4.1: This is the previous stable release. New releases are issued for critical bugfixes and security fixes. No significant new features are to be added to this series.
MySQL 4.0: This is the old stable release. This version is now retired, so new releases are issued only to fix extremely critical bugs (primarily security issues). You may continue using databases you have in the 4.0 format, however, you cannot upgrade a 4.0 version database to one of the newer database versions. You are always free to export your data from a 4.0 database and re-import into another database of one of the newer versions.
