More marginal corner-case uses for gems (similar to the amethyst/booze interaction):

• Throwing a diamond (or a diamond ring) at an opposite-sex foocubus will tame it.
• Rubbing an amber stone generates electricity, perhaps giving you a static charge that will add a bit of damage to your next melee attack.
• Hitting a demon with obsidian traps it as if it were a bear trap: it can’t move or teleport, though it can still attack. This also destroys the obsidian.
• Moonstone allows you to control lycanthropic shapeshifting. (Moonstone exists only as a ring in vanilla, not as a real gemstone.)
• Rubies and sapphires provide some very marginal protection against cold and fire respectively.