Galactica had various numbers of Vipers, some the old mark II that was also used in the first Cylon war, and some the newest mark VII designed for advanced avionics that was vulnerable to cyberattack. From watching the battles, it's not immediately clear what qualitative differences existed between the two models, and any differences in performance had more to do with the pilots than anything.
Still, there had to be some differences, even if it's hard to say whether one was better than the other. Certain pilots had a strong preference for one model over the other; Apollo was eager to transfer to a mark VII in the miniseries, whereas Starbuck flew the mark II (almost) exclusively, and Galactica had more than a few of each model so the aces could always pick.
Apart from the obvious cosmetic differences and avionics, are there any other differences? The BSG wiki is quite unclear, as the stats are virtually identical.