The section in Twilight Princess where you take the Zora prince guy to Kakariko Village. The bomb birds... the fires... trying to shoot arrows and throw boomerangs at the same time... all from horseback. Just no.
I would have to agree on Fire Emblem Awakening. That was a brilliant story, and I loved the ending.
I feel sad whenever I get to the end of a game/book/show with a great, captivating story. Kind of like a "Wow, what do I do with my life after that?!" feeling. But as far as games go, Zelda...
Wind Waker. Not only are the updated graphics gorgeous (and suit the art style nicely), but the minor tweaks to the Triforce hunt section and addition of the faster sail are fantastic improvements. No, it's not quite the same, but if you're going to remake something you may as well fix...
I don't really see the hate some people think it gets, but that may just be me. (I try to avoid hate, personally, which is a big reason for my limited participation in gaming forums.)
It has its low points, but overall I think it's a fantastic game. Not my personal favorite Zelda game, but...