Over all, i didn't use my Malachite Gems that often. i didn't want to waste a rare gem on a second rate piece of equipment just to juice my regeneration. i only ever used the Malachite Gems for the Rank 10 enchantments... like +100 Melee/Magic damage on my weaponry, +10 melee/ranged/magic armor on my gear.
by the end of DKS- ED specifically, i still have about 8... when i was done with FoV, i had almost 20.
I think you should use them as you need them, but wisely. 20 saved at the end of the game IS 20 wasted that could have at least been used on something.
