Before MySQL 5.1, the InnoDB storage engine was included by default when you compiled the sources. Since MySQL 5.1, it is necessary to set the storage engines to compile with MySQL with the parameter "--with-plugins":
--with-plugins=PLUGIN[[[,PLUGIN..]]]
Plugins to include in mysqld. (default is: none)
Must be a configuration name or a comma separated
list of plugins.
Available configurations are: none max max-no-ndb
all.
Available plugins are: partition daemon_example
ftexample archive blackhole csv example federated
heap ibmdb2i innobase myisam myisammrg ndbcluster.