LoZ - The Book of Magic
I'm pretty sure it actually makes the Magical Rod LESS effective against certain enemies. No thanks!
AoL - The Cross
You only need it to see blue eyes, and only in a couple parts of the game. You can beat the game without it.
ALttP - Ice Rod
The Ether Medallion did basically what this thing did, and did it better. The Ether Medallion was used to open a dungeon, too. The Fire Rod was used as a dungeon item, AND could kill enemies... but not this thing. It was only useful against Trinexx, near the end of the game.
LA - No useless items in this game. Okay, I guess I have to give Nintendo credit for this one, ALL the items are useful.
OoT - The Masks.
They don't really do anything. But they were still fun, and kind of foreshadowed Majora's Mask.
MM - The Circus Leader's Mask.
You can't get it until after you've helped Cremia without it, anyway, and all it does is stop the Gorman brothers from attacking you.
OOA/OOS - Still no useless items. I guess the limitations of the Game Boy's memory forced them to be efficient.
WW - The Telescope.
But it has sentimental value, and can help with role-playing, I guess.
MC - Yet again, no useless items. The GBA was still forcing them to be efficient.
TP - The Hawkeye.
I never needed it in the game, and I can't really imagine how it would be useful unless you were playing on a very small screen.
PH - The Fishing Rod and Big Catch Lure.
It's only used for a few sidequests.
ST - No useless items... again. The portable games have a pretty good reputation here.