Different gem stones hold different magical properties. Some examples would be a thaumaturge needing goshenite to augment their offensive magics, and a gladiator something with heliodor to increase their vitality. Something as simple as wearing the wrong ring whilst adventuring could result in your death.

[ Of course the more powerful the equipment the less important the gem stones become. Her strongest equipment has no gems in it that she can spot and is augmented only with materia. ]

Gems are also used as catalysts for summoning Carbuncles. You cannot summon a defensive Carbuncle with an emerald, just as you cannot summon an offensive Carbuncle with a topaz.