http://mysqldatabaseadministration.blogspot.com/2006/02/innodb-or-myisam-whats-your-preference.html
If there are many modifications of the data, it's said that InnoDB works faster because it uses row locking instead of table locking, like MyISAM. However, if there are mainly SELECT statements, a MyISAM table might be faster.
http://dev.mysql.com/doc/refman/5.0/en/converting-tables-to-innodb.html
Make sure that you do not fill up the tablespace: InnoDB tables require a lot more disk space than MyISAM tables. If an ALTER TABLE operation runs out of space, it starts a rollback, and that can take hours if it is disk-bound.
