In order to set InnoDB as the default storage engine in MySQL version 5.0.x the process is simple.
Open the my.cnf file in a text editor such as vi. If the following line is in the config it should be commented out or deleted:
Save the file and restart mysqld.
To verify that the default has been changed from MyISAM to InnoDB login to MySQL and run the following:
You should see that InnoDB is now the default.
+------------+---------+----------------------------------------------------------------+
| Engine | Support | Comment |
+------------+---------+----------------------------------------------------------------+
| MyISAM | YES | Default engine as of MySQL 3.23 with great performance |
| MEMORY | YES | Hash based, stored in memory, useful for temporary tables |
| InnoDB | DEFAULT | Supports transactions, row-level locking, and foreign keys |
| BerkeleyDB | YES | Supports transactions and page-level locking |
| BLACKHOLE | NO | /dev/null storage engine (anything you write to it disappears) |
| EXAMPLE | NO | Example storage engine |
| ARCHIVE | NO | Archive storage engine |
| CSV | NO | CSV storage engine |
| ndbcluster | NO | Clustered, fault-tolerant, memory-based tables |
| FEDERATED | NO | Federated MySQL storage engine |
| MRG_MYISAM | YES | Collection of identical MyISAM tables |
| ISAM | NO | Obsolete storage engine |
+------------+---------+----------------------------------------------------------------+