If you use a custom php.ini file on your site, you will lose Zend Optimizer functionality, as the custom php.ini settings remove the reference to Zend and Zend Optimizer settings in the server's default php.ini. In order to get it back, you will need to add the following lines to your php.ini file:
[Zend]
zend_extension="/usr/local/IonCube/ioncube_loader_lin_5.2.so"
zend_extension_ts="/usr/local/IonCube/ioncube_loader_lin_5.2_ts.so"
zend_extension_manager.optimizer=/usr/local/Zend/lib/Optimizer-3.3.0
zend_extension_manager.optimizer_ts=/usr/local/Zend/lib/Optimizer_TS-3.3.0
zend_optimizer.version=3.3.0
extension=pdo.so
extension=pdo_sqlite.so
extension=sqlite.so
extension=pdo_mysql.so
zend_extension=/usr/local/Zend/lib/ZendExtensionManager.so
zend_extension_ts=/usr/local/Zend/lib/ZendExtensionManager_TS.so
Note that this will also enable the Ioncube and PDO modules also.