You use them in Alchemy actually! They usually result in a "Jar of # Hearts", which simply gifts you a certain amount of hearts. The higher the Gem's level and the number used changes how many hearts you get. That's the only purpose I've found so far.
That is their sole purpose. If you combine 3 heart gems (and the higher the level the heart gem the more hearts) in Alchemy you will get the most hearts. Combining three 3 star items will get you the highest heart gem.