I'm currently working on a Drupal 6.x website that recently changed its database storage engine to InnoDB. I was not very aware at the time, but it does have some issues while running on Ubuntu.
Of course, I do all my development locally and I recently upgraded to the shiny new Ubuntu 11.04. For a while I blamed the ridiculously slow speed of this particular database to the OS upgrade, as, for some reason, I had to re-install my entire LAMP stack after the upgrade; the MyISAM to InnoDB switch happened around the same time.