This is my experience tuning a MySQL server running on Rimuhosting for Drupal.
First I installed a tuning script in /root
wget http://day32.com/MySQL/tuning-primer.sh
chmod 700 tuning-primer.sh
yum install bc
cp /etc/my.cnf /etc/my_$(date +"%Y-%m-%d").cnf
./tuning-primer.sh
Now add the following values under [mysqld]:
table_cache = 512
query_cache_size = 32M
query_cache_type = 1
max_heap_table_size = 32M
tmp_table_size = 64M
Here is some info: http://drupal.org/node/85768

This are probably not of general interest, just some example queries from a particular database that I wanted to save here as snippets.

--view all category titles from node: n & d, category node: c
$sql="SELECT n.nid, c.title AS cname, d.field_catcache_value AS cat FROM node AS n"
. " JOIN content_type_document AS d ON d.nid=n.nid AND d.vid=n.vid"
. " JOIN node AS c ON c.nid=d.field_category_nid"
. " WHERE n.type = 'document'";

--get the body of the category definition c from a given node n & d
SELECT n.nid, c.title, r.body AS cname FROM node AS n

pre{border:none;background-color:#f4f3d7;padding:1em;-moz-border-radius:10px}

<?php
exec("mysqldump -uDBUSER -pPASSWORD DBNAME > DBNAME.sql");
exec("tar -czvf BACKUP.tar.gz .");
print "Done";

First make sure the right packages are installed. With Ubuntu the benchmark gets installed with mysql-server. With Red Hat/CentOS you have to ask for it under servers/MySQL/benchmarks
Ensure MySQL is running with:
service mysqld start # Red Hat/CentOS
/etc/init.d/mysql start # Ubuntu

-create a user (such as backup) with select and lock priviledges for all databases from any host
-set MySQL server configuration to listen on external ports
pw=mybackuppassword
hst=MySQLhost
nice mysqldump -h $hst -u backup -p$pw --compress --add-drop-table --extended-insert -A | gzip -9 >/backups/$hst-$(date +"%Y%m%d").gz

phpMyBackupPro: No simpler backup for MySQL: http://www.linux.com/feature/127811
Tunnel to locally running mysql server using ssh:
http://www.nerdlogger.com/2008/06/tunnel-to-locally-running-mysql-server...
create and setup remote administrator:
first make sure that there are not multiple name@addresses where the user can log in, else every one will have to get permissions separately.
CREATE USER 'andrewfoo'@'192.168.1.%' IDENTIFIED BY 'foomatic';
GRANT ALL ON *.* to 'andrewfoo'@'192.168.1.%' WITH GRANT OPTION;