Good thread, but just to pick simon up on these points:
1) ionCube has been on the market since 2002, was the first PHP Encoder for the mass market, and is very well and widely known. A quick compare of the reach graph at alexa will show a similar reach (with the ionCube website recently having higher reach than Zend, but it swings either way as you'd expect), and the awareness of both solutions is probably about the same.
2) This is doubtful but do create a ticket on our site if you ever had any problems and hadn't done so already. In practice there could be occasional problems with any of the complex compiled code solutions, and Zend are not immune to their fair share as, for example, thread 19124 at the Zend forums shows where users were complaining that 64 bit support did not work for Zend Optimiser and that they would have to use ionCube instead. The Zend and ionCube encoding solutions are both highly complex, and the PHP group tinker with PHP internals constantly such that encoding solutions may occasionally need revising. In general though and on average you shouldn't find any difference between either in terms of reliability, nor any problem with either solution.
3) Both ionCube and Zend offer the same or similar back compatibility. Up until recently ionCube supported PHP 4 back to 4.0.6, which was the first feasible release of PHP 4, and PHP 5 back to 5.0.3 which was the first feasible version of PHP 5. It's also possible to run ionCube encoded files on PHP 5.0 that unencoded would only run on PHP 5.1 or higher. Some ionCube Loaders are no longer built for the very early versions of PHP 4, but could be if required. You'll also find that by special request and arrangement, ionCube Loaders can generally be built for platforms that are not officially supported, such as ARM processors and various embedded systems, and support for Mac 32 and 64 bit was provided long before Zend. ionCube Loaders for PHP 5.2 were also ready several weeks before Zend Optimiser for PHP 5.2.
While there are differences, both solutions should do the job.