Its impossible to come up with complete logical ordering for the reasons based before so I won't pretend my view is better than others. However there is one point I disagree with Erik (yes, again) is that I do think you have to take into evaluation the number of times teams have been competitive throughout the history of the cup. Of course there is a large discontinuity between the winner and the second place, and rightly so, but big teams are considered to be big because they have consistently showed their worth in Europe whether they won the tournament or not. For the same reason, there is no basis on which to regard Lyon, PSV, and to lesser extent Man U & Benfica into the same category with Juve. And by similar reasoning I do not consider Arsenal and Chelski to be a great team in anyway. Ditto for Aston Villa & Nottingham Forrest. Nobody considers Pro Vercelli to be a big team in Italia, for instance, despite how many Lo Scudetto they won back in the days. As they say form is temporary, class is permanent.
Having said that I consider Real, Bayern, Milan, Liverpool to be a superior team, and to lesser extent Ajax as well.