The percona-query-digest tool is excellent at tracking down queries that kill performance. The queries can be re-written on modified schemas with better indexes and you're golden. Once that's done you need to institure some healthy happy ways to avoid the problem continuing to recur through a little education and some development routines.
The simple way to ensure everyone uses the index Luke is to provide graphical feedback on the entire set of queries. The way to do this easily and cheaply is to use an open source tool called Anemometer. Download the source, install, configure and plug the shell scripts into your DB instance.
Once you have it running, you'll take the personal criticism element out of the equation. This is the primary reason for doing it. No one likes to hear that there query is garbage. You can avoid this awkwardness by providing everyone a tool that gives visual feedback. It's one of the most important disciplines that gets the least attention, particularly where the mountain of queries that Drupal can generate.
I wrote a simple blog about it, but this post gives you the idea. If you're having the same DB performance troubles due to a hurried pace like everyone else in the world, take a look at Anemometer as a way of stemming the Dev/DBA gap, rather than turning your DBA into a Dungeon Master. :)
Peace,

Comments
Hi. I'm interested in reading
Hi.
I'm interested in reading your blog post, but I'm having issues accessing your site. Any idea when it'll be back up?
It seems up from here.
It seems up from here.
Thanks for sharing!
Checking out anemometer right now.
Parallel workflow
As there is no doubt, its a wonderful module in Drupal. But as usual there is always a chance to make change and make things more & more better. For this hope, I'm thinking parallel workflow. and I want to work on this.