Winkler,
It occurs to me that the solution to your dilemma must be relative to who is asking for the procedure. For instance:
If this intended for a system like ISO9000, your answer might simply take the form of "say what you do and do what you say." By this, I mean that, 1) prior to the writing of any code, detailed documentation is generated stating the precise expectations of the new code. Then, 2) during the planning stage of the code, a check-list is submitted and approved detailing how the code is be verified (for example "With Machine in full Idle condition, push Start Button - Driven Roller A accelerates from 0 to 100 RPM"). 3) The code is then written and 4) the code is tested as per the check-list.
If, however, you are a machine builder and are looking to generally detail how the code will work for the customer, you will probably need the most detailed quote for the specific machine and develop a "do-this-and-expect-that" list. Rarely have I seen a customer actually wanting supplier to do "code" specific commissioning. Usually, the system as a whole is commissioned with the PLC code being nothing more than an internal component.
Finally, you could be looking at this from purely a machine builder's / programmer's vantage. If that is the case, I am not too sure any prewritten procedure will do much good. About all I can suggest is that you document each "thing" the new code should do, write a check-list of these things and then, during commissioning, demonstrate that it does them all.
With respect to hardware and the sequence of checking things out, I think seppoalanen's response is right on the mark.
Steve