I think the Deku Nut in Majora's Mask was highly useless (at least for me.) I don't recall having to use it at all (even as a Deku Scrub) so I have to say that. I do agree with some that it was more useful in OOT.
Oh, and the Blast Mask in MM was pretty useless too lol! (But that's not a multi-game item )
The lantern in TP. It helps you to see in the dark (obviously) but there's a map that tells you that you're still going in the right direction and once you get far enough in the game you can just turn into a wolf anytime and use your senses to light everything up. You sometimes need your lantern to get into certain treasure chests but you don't really need the rupees. (And if you do, you can cut the grass.)
The Giants Knife from OoT it breaks after 5 hits.
Magic powder in ALttP. Sure it gets you 1/2 magic but after that, what's the point? Turning enemies into funny characters? I can use the quake medallion to do that which is allot more interesting to use.