I linked Zivilin's post as a source: skill doesn't make much of a difference in regard to the damage of a hit. In throwing (or bows) what you hit is random.
So a bit of an expanded version of what Random_Dragon was getting at.
First the stuff we can control. Throwing damage is about ammo.
You want ammo that only has one attack (arrows, bolts, picks, war hammer, etc) rather than several (spear, short sword, battle axe and whatnot).
You'd consider the ammo's attack type (blunt or edge) in regard to its material type. A gold coin (blunt) may be better than a copper coin because it's heavier. Dense and heavy material types are better for blunt. If you've got bolts/arrows, the attack type is edge, so steel or bronze will be much better than copper or silver.
In cases where it's possible to view the raws, you'd want small contact areas for stabbing type edge attacks (arrows/bolts) or for blunt attacks. Arrows and bolts have a contact area of 5 which is overall the best given the conditions we want met. If your edge attack type is slashing, then you'd want the largest contact area with the greatest penetration (the large, serrated disc or the giant axe blade for example).
Now there are the factors we interact with but cannot control. The target's body material (could be meat, could be inorganic) and the presence or lack of clothing/armor. If you can ensure that your ammo will work effectively versus their clothing, armor, body material, then you improve the damage you might cause.