I run a site with 1.3 million monthly views and would be only too happy to run Skype affiliate but I also started the sign up process then was shocked that Commission Junction, asks me for my tax returns or numbers to be faxed to the USA. I'm not an American, I don't live in America. I think Skype as a European company should have looked for European affiliate programs, or at least ones that respect the world wide web and its people!
I would also advocate the use of cookies but combining with special URLs, so that in the event cookies are disabled there is still a shot at commissions.
I don't remember what it was now, but when I read up at the time several months ago, I was also not too impressed by some other things that did not seem much of an incentive to very popular sites and portals, but then I was adised to contact the responsible person at Skype. I did so, got an auto reply that he was on holiday and would reply on his return and have heard nothing since.