In my experience, thrown weapons are good for NPCs and bad for PCs.
The problems presented to a PC by a throwing weapon are multiple. First, he has only limited ammunition. Secondly, whenever he throws something he is throwing away something valuable. PC's are generally outnumbered and must be able to sustain long combats. And PC's generally have and need the advantage of superior gear, while at the same time are often in fights where they must flee, or where a weapon that misses the target is likely to end up in deep water or sailing off a cliff or otherwise become lost. It's just not sustainable to use expensive throwing weapons unless they have magical properties of returning, and its generally less effective to use thrown weapons than it is projectile weapons like slings and bows.
NPCs on the other hand can't expect to survive more than a couple of rounds, and generally have cheap gear. As such, it is viable to use thrown weapons. Light infantry with a half dozen darts or three javelins and a shield makes a viable skirmisher, with an AC bonus that a bow wielder wouldn't have. Heavy infantry can carry a javelin or spear and make a ranged attack before charging into melee and drawing a sword. Done correctly, that can give NPC mooks a minor tactical advantage resulting in a higher number of attack actions made prior to getting killed and can help negate the large advantages PC's have at ranged combat. As part of a general package of cunning and adept tactics, this lets you get the most out of your mooks without getting excessively cheesy.
Since you didn't tag the thread, I'm not sure what rules system you are using. But various things you might could do with thrown weapons include giving specialists higher rates of fire on light thrown weapons like shurikans, knives, and darts or having heavier thrown weapons potentially embed themselves in shields and armor and encumber the PC's until removed. You can also give tactical advantages to expert skirmishers in moving and defending themselves while moving, so that chasing down those javelin wielders is more frustrating, thus improving skirmishing as a strategy.