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.
Healing Orielle's Loftwing
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:
- Hearts (On flowers or on their own)
- Rupees (Green, Blue, and Red)
- Ammo (Seeds, Bombs)
- Catchables (Grasshoppers, Hornets, Rhino Beetles, Non-Blue Birds)
- Enemies (ChuChus, Bokoblins, Octorocks, Guays, Babas, Keese)
- Friendly Characters (Kikwis, The old lady in the temple, townspeople)
- Diggable holes
- Breakables (Pots, Bushes, big fruits)
- Other mushrooms (non-sparkling and sparkling)
- Bird Statues
- Other interactive items (Sticky Plant Bombs, Stamina Fruit, Chairs, Ropes, Trees, etc.)
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.