Crystals are generally valued for their rarity and usefulness. Sometimes just for the beauty, but commercially it's based on their color, clarity, cut, and carat of the crystal. These are known as the four Cs that are commonly used to grade gemstones. The color refers to the hue, saturation, and tone of the crystal. The clarity refers to the presence or absence of flaws, inclusions, or blemishes in the crystal. The cut refers to the shape, proportions, symmetry, and polish of the crystal. The carat refers to the weight or size of the crystal.
Some crystals are more valuable because they come from a specific location, have a unique back story, or are particularly scarce. For example, Kashmir sapphires are prized for their intense blue color and velvety luster, and are only found in a remote region of India. Diamonds are valued for their durability and brilliance, and are formed under extreme pressure and temperature deep in the earth. Alexandrite is a rare gemstone that changes color depending on the light source, and is only found in a few places in the world.
The metaphysical, spiritual, and healing properties of the crystal can also affect perceived value. For example, quartz is said to amplify, store, and transmit energy, and can be used for healing, meditation, and manifestation. Amethyst is said to promote peace, intuition, and protection, and can be used for balancing, cleansing, and calming etc.