Obviously, anything organic can be used for the making of meals and elixirs. I discovered at the first (and only, so far) fairy fountain I discovered that some of these items are needed to upgrade armor (so glad I had on hand what was needed). With the exception of the diamond I found, it looks like the other gems have some elemental quality which I'm guessing will translate into some kind of weapon or armor upgrade later in the game. I cheated and read about ancient armor. It looks like ancient cores and ancient shafts are needed. Do ancient gears and ancient screws have any practical uses? What about diamonds? Amber? I am trying to figure out if I have anything I should just sell 100% of when I find a merchant.