The difference is that, as far as I can see, mobiruby is a Ruby interpreter/VM embedded in an Obj-C application. This is in contrast to MacRuby which is implemented directly on top of the Obj-C runtime. So, MobiRuby still has to go through the work of converting Ruby objects into Obj-C objects, whereas in MacRuby a Ruby object is an Obj-C object.
For a practical example of what this means, see the most recent sample code that was released for mobiruby: https://gist.github.com/2577620
For a practical example of what this means, see the most recent sample code that was released for mobiruby: https://gist.github.com/2577620