Complete Divine covers destroying souls (Sphere of Annihilation) damaging them (barghest ability) When it comes to storing them though, trickier.

the sword Blackrazor from Arms and Equipment Guide consumes souls, and can feed some of that energy to the wielder, removing negative levels bestowed on him. Victims need wish, True Res, Miracle to bring back (and still only 50% chance)

Larvae are Souls of a sort- so slain evil victims souls can be used in spells as components, if you can get hold of them (portal to Lower Planes, maybe)