I spent over an hour in Skyview Temple because I was an idiot and didn't see that log there... You know what I'm talking about? It's the part where you have to raise the water level twice, so that the log can float upward and give you a platform to jump off of an reach the vines. I figured the water thing out just fine, and I knew that the Small Key HAD to be across the room in the chest I could see from the other side, but I wandered back and forth between the two rooms over there, trying to figure out how to get to it, because for some reason raising the water level didn't scream at me "HEY MAYBE SOMETHING IN THE WATER WILL HELP YOU REACH THERE."
EDIT: So... I just realized I have a lot of these. And I mean... A LOT.
For example, in Majora's Mask, during the Goron section of the Moon Child room, I was stuck forever because I couldn't do the "roll and bounce off the obstacles" thing. I looked it up and then realized that the way to get through it was just not move the analog stick in any direction. I was also stuck for forever on the way to Snowhead because I didn't have bombs and for some reason getting them at the Bomb Shop must have seemed absurd. Oh, and let's not forget that time in FSA where I made the perfectly logical conclusion that getting the Power Bracelet meant you could move graves, not GIANT TREES.
I know there are more, but that's all I've got off the top of my head.