Before I start, let it be known that this is mainly my opinion. (I just say so because I think everyone is taking this a bit too seriously)
As the Ocarina of Time fanboy I admit to be, I have to be perfectly honest: I can't help ignoring this. That said, I don't really care that Arkham City has taken its spot on Gamerankings, which in the end, is actually an opinion just like the one I'm expressing now. Except that it has major media support on its side, which in the long run is an advantage that won't really stay. In other words, it's not a good point to support the argument of either game being better.
Still, we all should've known that another game would take that spot. Yes, Ocarina of Time has had the spot for 13 years by now, but that never meant it was gonna keep it forever. Game design has advanced a fair bit since 1998, and even though it was a landmark in game design, that means it was a foundation for the design, not the top of it.
Now, if anybody thinks OoT should stay as the top game, let me ask you: What would that mean for Zelda as a whole? Does that mean we should just stay with that game being sorry about how they are not as good? I don't like that idea, and I personally think that every Zelda since OoT has outdone it greatly. Even the so-called "dissapointment" that a lot of people seem to think Twilight Princess was, but I guess that has to do with personal taste, something I will not argue against. Despite that, I still consider OoT to be a very special game because of the experience it gave me. To me, that is an advantage I doubt Arkham City will get, no matter how good it is (don't get me wrong, by the way. I think the game looks awesome).