So, for skyward sword I found:
1. one small chest on the goddess island in skyloft. once the island breaks and falls down I don't think you can get to this chest.
2.Sky keep has some miss able things. I remember I was skipped a room and I never got the map. Can't enter it anymore once the island has fallen.
The OoT section mentions that you can only hear the Scarecrow's Song at the end if you beat the game with zero deaths. But in OoT 3D, it doesn't count deaths, and even then I have been making an effort to not die in it. I'm just wondering, will I still hear the Scarecrow's Song in the remake?