Spirits-and-Crystals

Yep! In terms of energetic incompatibility, I've only read one account of proximity making a gemstone shatter - supposedly it was when someone's kid found two of the person's gems in a glass of water together by a sunny window and he switched one out for a different stone at random. According to the story, his mother checked on the glass a few hours later and she found one of her crystals cracked into pieces without it ever having been removed from the water.

Otherwise, from what I've read and experienced, most gems are synergistic with each other.

One precaution I'd recommend is looking up the hardness of your gems on the Mohs scale to see if any are easy to scratch or crack. If they are, giving those invididual stones their own little felt or velvet sheath will usually be enough to keep other gems from damaging them while they're being carried together.

I keep my moldavite and selenite in their own felt sleeves, since they're the most fragile ones I have, and the rest are loose.

Other than that... as long as you don't 'sense' that certain crystals don't want to be together, they'll be fine. And even if they do give you that message, sometimes all it means is one or more of the stones just needs an energy clearing/cleaning before it goes back with the rest.