You can get lots of topaz, venom stone, tiger's eye and sapphire on Sentinel Island. (Emerald too, which is pretty useless IMHO). Also save and reload before Lamotte until he has what you need in his inventory. Only he seems to have gems in this part of the game. This only works the first time you approach him after each level up. But I just keep reloading until he has what I want. This works with all the merchants I have tried.
