Please refer to http://www.debian-administration.org/articles/442
a well written tutorial, basically we should do are simply:
/etc/init.d/mysql stop
/usr/bin/mysqld_safe --skip-grant-tables &
mysql --user=root mysql
update user set Password=PASSWORD('new-password-here') WHERE User='root';
flush privileges;
exit
fg
Ctrl+C
/etc/init.d/mysql start