The 939 pin one is better than the 754 pin one because the 939 CPUs have newer tech and more features, like dual channel RAM capabilities. The 939 is not better just because it has more pins, though.
pin count is not a good indicator of how good a processor is like vybuni said. for instance i would say the pentium M/core duo is better than anything available on lga775 yet they are s479 processors. yes s939 is better though.