As it stands now, gems of great value aren't worth much more than the 40 or so platinum you'd get for selling them to a vendor. Though this used to be a lot back in the day, it's nothing in the current situation.
Why not make them usable to craft amulets, like the following:
Amulet of the Red Lion (Str + 1, Resist fire +5)
Requires:
1 Ruby of Great Value
1 Amulet
1 large gold nugget
Amulet of the Blue Falcon (Int +1, Resist Cold +5)
Requires:
1 Sapphire of Great Value
1 Amulet
1 wand
Amulet of the Green Dragon (Con +1, Resist Poison +5)
Requires:
1 Emerald of Great Value
1 Amulet
5 Mint Sprigs
Amulet of the White Tiger (Dex + 1, Resist Electricity +5)
Requires:
1 Diamond of Great Value
1 Amulet
4 pearls
It'd give a use for the items, plus, it would give mid-range amulets for those that can't afford something like the Blue/Red Dragon Amulet Fragments and things like that.