Keeping stuff clean is easy if you know the mohs hardness of the stones in question.
For any of the quartz group (mohs 6-7) and up, you can use just about anything and not damage the stones. I use an ammonia cleaner similar to Windex. The notable except here is emerald which can be so occluded that you shouldn't do anything more than dust it off.
For a really soft stone like calcite (which I love), keep it in a box. Even dust can abrade the stone.
The felspar group of stones is similar to quartz in hardness and can be treated with the same cleaners.
Do NOT use cleaners on pearls, opals or some emeralds. Sodalite will disintegrate in water since it is a salt.
When you buy a stone, simply google up your stones name and "mohs" and you'll get your stone's hardness on that scale. Any stone 6 and above on the scale is pretty tough unless terribly occluded.
HOpe that helps. If you have questions, please let me know.
p.s. none of this applies to raw specimens which might be damaged by exposure much less water.
