There are a few Zelda items that I find useless...
Nayru's Love (OoT):
This item creates a protective barrier around you for a limited time. Sounds useful, right? Well, you get it late in the game, when you would expect yourself to have many hearts, and OoT is by no means a hard game to begin with. Did I mention that it eats up a lot of magic per use?
Spinner (TP):
A skateboard crossed with a spinning top that rides along rails sure sounds like a good item. That is, until you realize that rails are few and far between and that the Spinner is completely impractical for attacking or travelling without those rails.
Dominion Rod (TP):
The thought of controlling statues is cool, but wait! There are only a handful of statues in the game. Also, you can't directly use it to attack, so most of the time it just sits in your inventory...