In this latest post from the PHP Security Blog, there's some interesting opionions about the Zend Encoder and ionCube Encoder.

From time to time people ask if it is possible to use the Hardening-Patch together with the IonCube Encoder or the ZendEncoder. I usually answer, that they should ask the IonCube support or the Zend support, to simply create compatible versions.

The IonCube Encoder does not offer any protection against oparray_dumping or oparray disassembly. The good news for all the users of ZendEncoder (or however it is called nowadays) is, that it is a little bit harder to get the disassembly of scripts that were encoded with ZendEncoder, because you will notice that the Opcodes are encrypted.

According to this post, there's a few things to watch out for when you use these encoders, including the ways to get around them...