Opaque gemstones like lapis lazuli, turquoise, and malachite require special care. Never use an ultrasonic cleaner and never use ammonia or any chemical solution. These gem materials should just be wiped clean gently with a moist cloth. The gemstones can be porous and may absorb chemicals, even soap, and they may build up inside the stone and discolor it. The reason why these materials need more care than transparent gemstones is that these materials are essentially rocks, not crystals of a single mineral.
Opals also require special care.
Never use an ultrasonic cleaner, never use ammonia, and avoid heat and strong light which can dry out the water in opals. Organic gems like pearls, coral, and amber should only be wiped clean with a moist cloth. Due to their organic nature, these gems are both soft and porous. Store each piece of gemstone jewelry separately so that harder stones don't scratch softer ones. Almost every gemstone is much harder than the metal it is set in.