I'm gonna have to disagree on a couple of these, here. Like the Cross. Um, it makes the game much easier to beat, as the entire Valley of Death is littered with invisible Moas (which are enough of a pain when visible). Not useless at all. The most useless item in AoL would be the Whistle. Yeah...
The bombchus were useless in both games. They only had two actual uses in each. Well, actually, they didn't need to be used at all in Majora's Mask to beat the game. But still...
And Magic Powder wasn't useless. That stuff did a lot of useful things.