I can appreciate the influence that Ocarina of Time (and other titles such as FFVII) has had on modern gaming, but I honestly think OOT has long since been surpassed by other Zelda titles, and others as well. It was a skeletal framework. It's been years since it was released, and things have gotten better as the formula has been refined and improved. Just because it was the first (or, rather, the first one that was recognized by a huge number of people) does NOT mean it was the best; far from it in fact.
I think that is one of the primary reasons lists like these bother me - they're stuck in the past. Nothing can ever be as good as the first one, and if you even think otherwise you're obviously wrong. Voice it and you're liable to be burnt at the stake for heresy. If I had the kind of attitude Empire and IGN have, I'd never play newer games at all. The whole idea is that things improve over time, and I think that should be recognized. Really, the list should be called either "Most Influential Games Of All Time" or "Most Popular Games Of All Time" rather than the "Greatest".
I wouldn't say it was overrated, but poorly represented by the media and the fanbase? Absolutely.