I found this quite interesting but I have not yet had chance to apply / test : http://www.percona.com/webinars/2012-03 ... iguration/
I also haven't had opportunity to do any testing of the percona rebuilds of MySQL server but they look pretty promising!
The my.cnf is highly dependent on server spec, environment (shared,dedicated,dedicated db server) and what is being hosted. For example we have a fairly high innodb_buffer_pool size as the applications we host tend to use innodb heavily.
You may (or may not) find increasing this has an effect, since it looks to be set at the default of 8MB (ours is specified at 1GB on our 8GB shared servers to give you a comparison). However if its not used it makes little difference. That said, the psa database uses it heavily and its the default engine in MySQL 5.5
Also "old_passwords=1" is in the default CentOS my.cnf's and all our configs... which is posing an irritating problem when moving to PHP 5.3 and php-mysqlnd specifically, as its not compatible and requires reapplying of MySQL user passwords to create new hashes.