I decided to vote for the Giant's Knife in Ocarina of Time as the most useless item in the series. You buy it, yay, great, you have an extremely powerful weapon! Until you attack with it a couple of times and it destroy's itself. I really didn't see the point in that weapon, especially since if you took the extra time to take part in the Biggoron's sidequest, you got the same weapon that was unbreakable. That fact makes the Giant's Knife the most useless game in the series for my eye's, as not only does it just break after a short amount of useage, but there are other weapons in the game that are exactly the same but don't break.
Although if you were to count the Magic Armour in Twilight Princess as an item, that would be a close contender for the most useless item in the series outside of completing Twilight Princess 100%. It would probably be useful if you could acquire it early on in the game for those gamers that aren't to good at playing the game, however, you don't. By the time you get the Magic Armour, you have already improved your skill at the game greatly, and therefore this item usually becomes void. The majority of the time I get it after I've beaten Ganondorf too...