What are best practices for Drupal 7 my.conf settings? I posted the following wiki to GDO to try to consolidate best practices for Drupal implementations:
http://groups.drupal.org/node/289613

There's just so much written out there, but the documentation is often old or very personalized to one person's my.conf file.

What have other folks used.  Starting with https://tools.percona.com/wizard seems to be the best approach, but the Wizard doesn't know anything about Drupal.
You need to profile this yourself, every server is different - there's not really any such thing as 'best practice' here; get mysqltuner up and running, and follow the recommendations. 

Don't try to think of it in terms of Drupal, rather in terms of any web application which needs optimising. If you get too hung up on the 'Drupal' aspect you'll end up looking in the wrong places to optimise