If you only want to run 2 cards then it doesn't matter, both would run at the speeds in the first brackets (x16/x16). But if you wanted to run 3 then the second board would be better. You would see a bit of a performance increase by going with the second one running 3 cards as long as your running some mid cards like HD 5770s or better.
I would not recommend 3 cards though as it doesn't scale well past 2 cards. So if the first is much cheaper then get it. Don't waste money on stuff you don't need.