In most cases, InnoDB is the correct choice for a Drupal site. It provides increased concurrency, enhanced performance and much more data integrity than MyISAM ever can. However, the pluggable nature of MySQL engines allows the user to "mix and match" table engines inside a single database. This allows us to consider tables whose workloads fit MyISAM more so than InnoDB. The main candidates for MyISAM in a mostly InnoDB-centric database are the search tables.