How can I set default storage engine used by MySQL?

Quoting the Reference Manual (Setting the Storage Engine):

If you omit the ENGINE option, the default storage engine is used. Normally, this is MyISAM, but you can change it by using the --default-storage-engine server startup option, or by setting the default-storage-engine option in the my.cnf configuration file.

The default-storage-engine option must be part of the mysqld section in my.cnf;

[mysqld]
default-storage-engine = innodb

You may also want to change the default storage engine just for the current session. You can do this by setting the storage_engine variable:

SET storage_engine=INNODB;

you need to specify the default storage engine when starting mysqld. for example:

mysqld --default-storage-engine=InnoDB

http://dev.mysql.com/doc/refman/5.1/en/server-options.html#option_mysqld_default-storage-engine