mysql> SHOW ENGINES;
+------------+---------+----------------------------------------------------------------+--------------+------+------------+
| Engine | Support | Comment | Transactions | XA | Savepoints |
+------------+---------+----------------------------------------------------------------+--------------+------+------------+
| InnoDB | YES | Supports transactions, row-level locking, and foreign keys | YES | YES | YES |
| MRG_MYISAM | YES | Collection of identical MyISAM tables | NO | NO | NO |
| BLACKHOLE | YES | /dev/null storage engine (anything you write to it disappears) | NO | NO | NO |
| CSV | YES | CSV storage engine | NO | NO | NO |
| MEMORY | YES | Hash based, stored in memory, useful for temporary tables | NO | NO | NO |
| FEDERATED | NO | Federated MySQL storage engine | NULL | NULL | NULL |
| ARCHIVE | YES | Archive storage engine | NO | NO | NO |
| MyISAM | DEFAULT | Default engine as of MySQL 3.23 with great performance | NO | NO | NO |
+------------+---------+----------------------------------------------------------------+--------------+------+------------+
Osobně vždy používám InnoDB, pokud musím používat MySQL. Podporuje transakce a cizí klíče, zatímco MyISAM ne.