We still don't know if transmuting is in but too many gems were definitely not a problem in the beta. They were great for socketing in throwaway stuff, great to sell for gold and the few you actually might want to hold onto were worth the inventory space.
“Watch your thoughts; they become words. Watch your words; they become actions. Watch your actions; they become habit. Watch your habits; they become character. Watch your character; it becomes your destiny.” ― Lao Tzu
Why didn't you use them, transmute them, or sell them? Aside from their own useful properties, which are make wasted space if you don't start socketing some of them, ember is some of the highest 'gold density' reward material in the game. Sell them and use the GP's for your own choices of stuff.