It means the person writing the patent does not want to limit his invention to any aspect he describes and patent as many aspects as possible and underline that the embodiments are just examples. It's part of the way of writing a patent, most attorneys use phrases like this.
Computer software embodied in a computer-readable medium means exactly what it says -> they want to patent the software. This is just the normnal way of saying it, because software patents are not allowed in some jurisdictions and depend on altering the physical world in others. In the end, just take it literal. Software always is on a computer-readable medium, everything else would make no sense.
Apparatus is the machine, method the process of using it and software the implementation. By patenting all three they can possibly catch implementations that infringe with an altered software or an altered process or something like that. Sometimes claims like this are worded "a device configured to do this and that" - in this case the device doesn't even have to do it, it just has to be able to do it to infringe.
Things like this are the reason a patent attorney should draft a patent, experience is needed to write a good patent including this stuff and understanding what it is for.