Another factor in favor of Cokin for me is that I have lenses with 77mm, 67mm, 62mm, 58mm, and even 52mm with the new EOS M. With a Cokin P system, you can buy the filters once and get adapter rings for your lenses. They are a bit bigger than the screw in ones, but holy cow, you could go bankrupt buying good quality circular polarizers for your whole lens collection. With Cokin P, if you get a new lens with an odd filter ring size, your total cost to adapt your filters to it is a $20 ring.
One thing to consider is that the P series doesn't work with the widest angle lenses. I don't have a 16-35mm or 17-40mm, and I think they work down to about the widest on those lenses, but I am not sure about that.
I was going to mention the Lee system, but I see you edited your response as I was finding some links I switched from the Cokin to the Lee system because it has wide angle adapter rings (49 through 82mm). I use them with my 17-40L and can stack 2 filters fine.