I don't like a completely useless item, but I actually don't mind if it's only useful in one dungeon. I think having items that are fairly reusable and dungeons that are non-linear are somewhat at odds with each other. The more an item is used in later dungeons, the more important it becomes to pick up that item first.
I think one attempt at achieving both would be to have some dungeons that didn't rely on previous dungeon items, but have optional dungeons in the overworld that did. For example, I really liked those labyrinth-caves in TP (one in Hyrule field, one at Lake Hylia). Adding an extra would have been a good way to bring items like the spinner and double clawshot into effect. The double clawshot would have also been an excellent opportunity to bring some rock climbing into play.
Anyway, I also like Xinnamin's idea of upgrading items so they had more than one use, particularly if they made it so that some puzzles could be solved in more than one way. That way the items could be reused but it could also up the potential for nonlinearity if some of the usage overlapped. (Not too much, though, otherwise they would just become redundant.)