Use InnoDB for all tables, unless you can prove a compelling performance advantage for using MyISAM, or you need MyISAM's FULLTEXT or GIS indexes.
InnoDB is the default storage engine in MySQL 5.5 and later. InnoDB is crash-safe, and it is being developed actively. And it has better performance than MyISAM in most cases.
MyISAM gets corrupted easily during a crash. It does not save data to disk synchronously (relies on filesystem buffering). It has only table-level locking. It is receiving no development or enhancement, and it's on its way to becoming deprecated.