Is it permissible to sell copies of a pre-made computer program – that require no effort to copy – after exerting effort in creating the original version, whether the sale is to a limited number of customers or permanently online?

There is no blame in earning a living from what you create in terms of programs, whether original discs or copies of them, because it is the fruit of your effort in designing the programs, and therefore the design of programs has financially-recognized rights according to Islamic law.