I agree with some points made. No, I wouldn't include teams like Delta State or Immaculata, they had truly no longevity. La Tech and ODU had good longevity, not necessarily at the highest level, but arguably over 20 years of respectable success. I think ranking the greatest programs of all time, as was pointed out above, is dependent on what factors you value.
The only thing that leapt out at me was I thought Purdue was a bit high. As someone else said - JMU? Not sure on that. A case could be made for Oklahoma as someone pointed out. Although Auburn had a very good run under Joe Ciampi, I think it is difficult to rank them over other programs with perhaps longer term success. It is all a very tough call.