MyISAM versus InnoDB tables
Unless you have a specific table that needs a a MyISAM-specific feature such as fulltext indexes, you almost certainly want to use InnoDB.
If you think you have a special case that makes MyISAM a better choice - you probably don't (unless you're an experienced MySQL developer, in which case you're probably not reading this article).
As of MySQL 5.5, InnoDB is the default storage engine. You may be interested in reading InnoDB as the Default MySQL Storage Engine.
To quote an old old conversation from #mysql,
<archivist_emc> busy sites with inserts should use innodb <domas> very busy sites with no inserts should use innodb too <thumbs> idle sites with no inserts should use innodb too <adaptr> servers without mysql should use innodb too