I have a program in mind that creates breeding charts.
You would have to input a range of pokemon (from the same egg group) that you've caught, including gender, species, nature, maxed/usable IV's and such and then specify what you want them to breed into like for example a female mudkip, careful nature, 6x31 IV's, egg moves, maybe an extra option for Hidden Power and so on.
The program would then create some sort of chart that tells you which pokemon you have to breed together in what order and would give you the option to keep track of what you've already done (highlight pokemon that have already been bred, that are currently being hatched, that are breeding at the moment).
You would also have to input the gender of pokemon that have just been hatched so that the program could adjust the chart and tell you which gender the respective next breeding partner needs to be manipulated to.