Gems are meant to be spent and the two schools and three fruit trees are an excellent investment.
I also like the black sheep as a gem purchase. It always drops prime cuts, which allows you to get random stuff from the Feed the Baron recipe.
But do that after the wizard schools and fruit trees!
Never save gems for later. Once you have enough gems for something buy it immediately due to their business model of forcing you to accidentally lose gems throughout every game.
I'd suggest 1-2 wizard schools, one of each of the fruit trees and then an additional glimmerdust trove if you still have spare gems left.
I'll go for 2 wizard school... The animals and fruit trees can drop from adventure, though very rare...
2 wizard schools (make sure to update both to the highest level), then trees.
+1 on the two schools first.
As for trees and animals, they drop from adventures so you'd eventually end up having many of them. I say, after wizard school, choose the tree or animal that gives you what you need now. At the time I bought an apple tree and a black sheep because they would help me get through some goals I was stuck with. Now I have got five other apple trees and one more black sheep from adventures, yet I don't regret my nvestment because the two I bought with gems were really helpful for me then.
I don't typically use my gems unless I get caught in a gem trap. Here are items I have purchased with gems:
1. Orange tree (1) - I'm considering an apple and lemon tree so I can finish the food quest with lemonade and apple pies.
2. Wizard School (1) - I have 40 energy, so I didn't feel a need to buy the second one since I only utilize the wizard school as much for energy.
That's it! Like I said before, I'm considering buying the apple and lemon trees as well as a sheep (just to have one of each animal besides the elusive Alicorn). I haven't been able to justify purchasing the Royal Manor as I have enough royal points to get me through all present goals. I was considering buying the valentine's animals but I just received a cupid pig from an adventure, so I'm holding off for a little bit.