Remember that the criteria for this list is based more on how much the game influenced a genre or the gaming world moreso than how great a game is (although the latter weighs heavily as well). Thus, Ocarina Of Time was given the #2 (not Wind Waker, even if it is the better game) because it had a tremendous influence on 3d games, huge environments, camera angles, controls & camera, graphics, etc. Mario Bros was #1 because it is the very game that defined modern games. It is the "mother" really of the games and platformers we play today, even if there were games before it. And Super Metroid and Metroid Prime were listed separately because they each added different things. Ocarina Of Time and Wind Waker were mentioned together because the things they have established in the gaming world are quite similar in many regards.
I was really impressed with this list. One of the best Top 100 lists I've seen, and they kept to their criteria well. It was nice to see Chrono Trigger at #12, the second best RPG on the list, and only because FF2 (or 4) was really the first huge modern type RPG. FF2 really brought character development and plot development to the fore, and was one of the first to do so. Chrono Trigger is perhaps gaming perfection, especially for RPG's. It took everything and made it PERFECT. It is still considered by many, including myself, not only the best RPG ever, but also the best game ever. If it was a best game list, I would have liked to see it higher, but it was a perfect placement based on the criteria IGN set for the list.