Quoting Ivan Sergio Borgonovo mail@webthatworks.it:
It really depends on what you need to do. If you don't know it I'd go for MyISAM since most of the features you may be looking for in InnoDB are not really fully exploited by stock Drupal.
Well, not yet anyway. http://drupal.org/node/301362
-- Earnie http://r-feed.com Make a Drupal difference and review core patches.