They are for adding Special Abilities to C, B, A, S grade (non-dual swords) weapons.
To use them you must have the lvl 40 quest "Enhance my Weapon".
Use the crystal when a mobs HP has dropped below 50%. Then make sure you're the one who gets teh finishing blow. You then have a chance of staging it or blowing it. Different weapons require different Stages/colors. Take your weapon to a head blacksmith to see what crystal you need.
You use them to put Special Abilities (SA's) on C-grade and higher weapons. There is a quest involved to get the Soul Crystals and raise them up to an appropriate level dependant on the weapon.
That was a C3 quest change I believe. Others have posted the same thing.
If I remember correctly it gives you a stage 3 or 4 crystal. They're not useful untill they hit stage 5 and then it depends on the weapon/grade. Either sell it for 100K times the stage, or save it untill lvl 40 when you can lvl it higher.