Damn, running low on Nerd Rage/Rant here... let's see if I can tackle this thread without screwing up, especially since it's the reason I freaking registered, finally.
Which game is darker? Well, I suppose it's subjective, to be perfectly frank. From a realistic standpoint, Ocarina with it's "seven years of darkness" is arguably way darker than anything from the "three days to eternity" that is Majora's Mask. However, since all that is speculation, as we don't specifically see or hear about many of the atrocities we conclude occurred in that seven years, we must therefore look at what we DO know happened. Because Ocarina of Time just didn't have the character development or depth that Majora's Mask had, most of what we know is either visual first hand experience or simply seeing the end results.
-Ocarina of Time-
Those "child days" or whatever you wish to call Young Link's time, were pretty damned idyllic with little in the way of strife or problems, especially since Link went and solved all the problems by helping out the Gorons, Zora, and arguably the Kokiri as well. The only real darkness we see is that Gannondorf was mean to the Gorons by blocking their access to food, which could easilly be circumvented by the Gorons owning it up and eating less palattable foods until an inevitable solution is found.
He also see that he poisoned the Great Deku Tree, though again this is all just stuff we're told, which would eventually lead to the death of said guardian although a sprout is planted which'll eventually become the next Great Deku Tree and arguably has all of the previous entity's memories (though probably not his personality). I'm not even sure at the moment if Gannondorf had anything to do with JabuJabu and the Zora in general, but that's merely my memory failing me at the moment. He may have been responsible for making JabuJabu sick, I just don't remember right now. Hell, according to the one Zelda Manga (that official one I really liked), she went in there to get away from an arranged marriage. Who knows, but I'm sticking to the game for this.
Then Gannondorf chases after Zelda and blasts Link, both of which lead to nothing as Link is seemingly unphased and he is unable to capture Zelda. Nor does the castle town or its carefree inhabitents seem to remark on the "attack" in any way. Flash forwards to the future. Yes, we see the end results of the down being destroyed and deserted (unless those ReDead are the people, which isn't a bad theory but no proof), we see the crater where Hyrule Castle once stood. Again, this is just us seeing the result, not the actions. In general, yes, the entirity of the future part of the game is fairly darker than the first half, but that's a given.
Also just because the Shadow Temple is ghastly doesn't necessarilly mean the game or storyline are much darker. That had nothing to do with Gannondorf insofar as we know. I believe we were told at one point a great evil was sealed under there and G-dorf simply let it out, he didn't redecorate the place. Not only that, but while there was a lot of oppression, sure, you don't exactly see a lot of people DEAD as a result. The Kokiri children are still alive, the Zoras are all alive merely frozen, and you rescue all the Gorons. Again, these are all happy-ish endings to otherwise bleak scenarios. As someone else said in this thread, Ocarina of Time has a constant "hope is always there" vibe to it. And you can't exactly call that... ending... dark when it has every friggin person in the game outside DANCING, even when it breaks their character or seems out of place. That's about as happy and cheerful as you can get.
-Majora's Mask-
This game... it sucks the joy out of you. It beats you in the face with how horrid and cruel the Skull Kid is when under the influence of Majora's Mask. Gannondorf had seven long years to corrupt Hyrule, while this one boy caused pain and suffering and agony in a few short days. He single-handedly caused the death of all three characters you turned into, and in the case of the Deku child, we're treated to this depressing, pathetic looking, seemingly dead tree with a face. All Tatl has to say is "How sad, doesn't he look kind of like you?" for us to realize that the Skull Kid was responsible for that. We don't even get told what cruelty befell that poor child before he was turned into that either. He set everything in motion for both the deaths of Mikau and Darmani, as he was the one who told the Gerudo they should steal the eggs, and was very likely the one who put Big Goron on top of Snowhead seemingly under an enchantment. BigGoron even says "How'd I get up here? I was on my way to see what was keeping Spring from coming".
But even looking past those events, we have everything else. A little girl who, without Link's intervention, would fail trying to protect her farm's cows and be abducted with them only to be returned a day later not recognizing anyone and just staring blankly into space. Not to mention how the Gorman brothers were attacking and stealing/destroying Romani's milk and gods only knows what woulda actually happened to her if Link hadn't been there to protect the wagon. She coulda been killed. We have no real indication as to what deaths were caused by the poisoning of the Southern Swamp, the endless winter in the mountains, or the clouded waters in the ocean, but I'd hazard that some people did die. We have no proof that those Gerudo we see failing to make it into the Great Bay Temple survived, either. There's Anju and Kafei whose love is doomed even as the moon slowly bears down upon them. Do I even need to mention that scene when you help them, and he shows up at the last moment, so they can be in each others arms "as the moon crashes down and kills them all"? That scene made me cry when I first saw it back in high school, it was so depressingly sad.
These are the things that make me say Majora's Mask is a lot darker than Ocarina of Time. In the former, hope is alive and your actions are apparent as whole peoples are saved by them. You have a very cheery first portion of the game and a corrupted, but not overly "depressing" future in the later portion as a result of many things being "undone" by Link's actions. In the latter, the very beginning of the game is bleak with the threat of impending doom looming over you for the entire game. All your actions seem for naught as it doesn't return those who died, it doesn't stop the moon from crashing down (during the normal gameplay, not the ending, I mean), and everything you do is undone simply by saving your game and going back to the first day again. You see and feel and experience much of the suffering and pain the characters endure in Majora's Mask, while we're simply told about it in Ocarina of Time.
So yes, on one hand we have seven years of darkness with no end in sight, but hope is always alive in your character and his actions. And in the other we have people who know their misery will end in three short days, so let's make them as miserable as possible before then. It would certainly seem from those two sentences that Ocarina is the darker game. But looking at the games themselves would show you that Majora is a lot deeper and darker than the other could ever be.
Personally, I'd blame it on the very flaws inherent within Ocarina that caused Majora to be made in the first place. A lack of general character depth and development combined with a lackluster ending, so the sequal is full of depth with characters having their own stories and problems whom you get to know, therefore caring a great deal about them.
