Our database management service team got a similar request two years back when we had to upgrade MySQL version 4.0 to MySQL 5.0. We are listing here the same approach for the current needs of upgrading MySQL 5.0 to 5.1
File responsible for the MySQL version is /var/cpanel/cpanel.config
Open it, find the variable mysql-version and edit the value to read mysql-version=5.1
And finally run
/scripts/mysqlup
This should upgrade your MySQL version to MySQL 5.1. For better understanding of the process behind, /scripts/mysqlup, go through the code and browse the URL http://httpupdate.cpanel.net/mysqlinstall/
NB : Chances are that, upgrading MySQL may break the php and in such cases, do recompile php, using easyapache or your custom compilation methods.
