This list is ridiculously Nintendo-centric. In some sense, it is interesting to look through. But, it certainly cannot be taken as a serious ranking of the greatest games ever made.
Looking at the games in the Top 100, most have under 10 votes total which means it wouldn't be too hard to make the list more diverse if a couple more Playstation leaning users submitted their lists.
Of course, it's not just about the amount of votes, but the value of each vote too - for example, while Metroid: Zero Mission is at #83 with 10 votes, Final Fantasy VIII made it to #74 with only 5.
Ultimately, though, the beauty of this event in my opinion is in sharing our own opinions about the games each of us love. What matters most to me is each person's individual list, and it bothers me that there are people (RolStoppable) who would specifically design their lists to affect the end results. But, oh well.
Obviously this shouldn't be taken as a serious ranking of the greatest games ever made. It's a reflection of the current state of the VGC community, and which fanbases are more active in it. That said, I'm not sure any "greatest games ever" ranking can be taken seriously at all, because objectivity doesn't really exist.