Eeeeh..... there are a few. Like the Wind Fish's Egg in Link's Awakening. An egg... heh. When something hatches, it's life in the egg ends, and its life in the "new world" begins. I think it was fitting for the plot of LA.
I did like the ring of fire around Death Mountain in Ocarina of Time. When you wake up an adult, you know things are different. You worry what happened to Zelda. Has Ganondorf done anything yet? And then you get outside the Temple of Time right after being spooked by the very mysterious Sheik for the first time, and that ring of fire is there, and you just know something horrible has happened. It was awesome.
The moon.... eeeh, I'm sorry, but it really only made me take the issue less seriously. They just had to put a face on it. It cracked me up, and I still think it's a really goofy thing to try to put in something that was meant to be taken a little more seriously.
So far, I think seeing a big wall of Twilight is the best "landmark". I think it'd have been better if it moved at a more ominous pace, but eh, that' mean including a time feature again, and once was enough. In any case, I think it was pretty foreboding, and despite my issues with TP, I have to say that was pretty well done. Now if only the NPCs would've reacted to it and made the situation seem a little more dire....