The Intel DG41WV is a newer motherboard, which has PCIe x2.0 x16 and the older Gigabyte G41MT-S2 does not have it. It is only PCIe x16. There will be little to difference in performance between the two.
not necessarily. You would only see a performance increase if your video card required more bandwidth that what PCIe 1.0 could offer. I do not think that is the case as PCIe 1.0 has 2.5 GT/s. PCIe 2.0 is good for flexibility if you want to upgrade but PCIe 2.0 is backwards compatible.