Personally, what I think of, for stone transformation, I think shield. Perhaps, if you're doing a mirror shield, when you reflect light on them... they change. This would be effective against some types of enemies, npcs, and doors, like in MM / OOT. Persay, we have an eyegore. *now this doesn't have to be any old normal light.* There's a well of light, and you sit there with your shield, and you have to lure it near the light, and use either your mirror shield or other item of light magnifying ability.
Or it could be something like in MC, but controlled by being in, around or near some amplifying effect, where you charge up with the surrounding energy, and let loose a beam. This gives you many versatile options, such as, a firey torch for light, make it a fire beam. Plain light, affects stone beasties. Icy Torches, like in MM and OOT, shoot icy beams.
It could be an item or a sword, such as the shield in OOT, against the Twinrova sisters.
I don't know, it's just a though.