If you haven't already heard, Drupal 7 will default to using the InnoDB storage engine instead of MyISAM for MySQL (though a MyISAM database will continue to work just fine in Drupal 7). This is fairly substantial change within Drupal core, and as the thread in the issue queue I linked to shows, there were a lot of questions and apprehension about it. However...
...we are going to just skip over a lot of that apprehension and get down to point of this article - there's no good reason not to hop right into using InnoDB today on your Drupal 5 or Drupal 6 site. The rewards are; a possibly significant improvement in performance, a definite improvement in scalability (most highly trafficked Drupal sites have been using InnoDB for some time now because of this), and you'll start getting used to working with what will be more and more common in your Drupal-life, InnoDB.
I came to the conclusion about how great InnoDB is after researching the experiences of others, and after converting a large Pressflow-driven Drupal 5 site from InnoDB vs MyISAM. This change resulted in a 14% increased throughput during load tests performed in JMeter. That's a very substantial increase, and while everyone's mileage will vary based on their own site, server, and any number of variables it's clear enough to me that there's nothing to be afraid of as far as InnoDB goes (quite the contrary).
Converting your database to InnoDB
Before you go any further backup your database before doing any steps below. If you 'splode your database for any reason, you'll need it.
Here are the steps:
1. Shutdown MySQL
2. Move/copy/change the name of ib_logfile0 and ib_logfile1 files. (find where MySQL exists on your system - locations can vary greatly). MySQL will recreate these files when you start it up again. Not anytime you change the innodb_log_file_size parameter you will need to shutdown MySQL, move these files, and start up MySQL again.
3. Tune it up a bit
Based on a lot of searching around and benchmarking with JMeter I arrived at the setting below for running on my Macbook Pro. See the links at the end of this post for articles which can help you determine what to adjust these numbers to for other machines (ones with more RAM/CPU, for instance. The production server for this particular site ended up with 5000M setting for innodb_buffer_pool_size. So settings will, and should, vary greatly just depending).