After reading this question, I went and tried it; and, while it worked, I can't find a use for them. I can't sell them at the Item Check, and I tried poring them out, and it makes a yellow dust, but I don't know what that does.
I did the one quest after completing the third dungeon where
That one lady needs them to heal her Loftwing,
but
her brother gives you some with a free bottle, and as far as I know, my Loftwing can't get hurt.
What is their use?
Best Answer
If you're asking about the plain old Mushroom Spores, the spores you get from any plain mushroom, then I'm convinced that they serve no other purpose in the game and only have a one time use.
I've done a fair amount of testing and could not find a single use for them. Everything I've tried it on does absolutely nothing:
If on the other hand you are asking about the Glittering Spores, the spores you get from the glittering mushrooms, they have very limited uses AFAIK. There's only a couple of uses that I know of.
You can use it on Hearts or Rupees to change them. Hearts turn into Fairies. Rupees turn into different valued rupees, even a Rupoor.
On some of the smaller enemies, it knocks them dizzy. I was only able to do this on Bokoblins, Octorocks and Babas (the plants) but didn't have enough to test on others.