I have a tie between the Dominion Rod, The Slingshot, & Epona's charm-all of which are from TP.
The Dominion Rod was cool at first since u could use it to control that statue with the hammer. I had a ball with it...until we left th Temple of Time. We just gathered some letters after that, making it a very stupid item. I could see alot of potential with it & since it was in the Temple of Time, where the Master Sword was, & it also helping us getting to the Sky, I hope to see at least a easter egg of it in Skyward Sword.
The slingshot was ultimitly a huge fail in this game. You only used it in the Forest Temple/Dungeon & the only enemy that it could kill were the Walltulas. Then, as if it was a joke, all the way at the bottom of a small cave at Hyrule lake (if it has a different name, please tell me cuz I kinda thought it did too) lies a chest with slingshot ammo...(WHAT THE HELL)!? Weird enough, they also do that at Hyrule Castle of TP. If u managed to get all the keys, you can open a goodies room with a bunch of Rupees, Arrows and...slingshot ammo (Again, WHAT THE HELL)!?
And last Epona's charm. After Ilia finally gets her memory back & we see a very sweet seen of her memory, she gives Link Epona's charm that she was originally going to give him before he started his journey. At This point of the game, its almost completely useless, since Link could just warp from portal to portal with Midna. I thought this would of been ALOT more helpful if she gave it to Link when she was suppose to, it would of been alot more useful.
But if i have to single out one of them out of the entire series, it would be the Dominion Rod. If it was just limited to TP, then I would say the Slingshot