you can use resource folders. create a folder called resources and put all assets that you want to get reference to them by their names, in that folder. use the Load method to load resources. example let's say you have a prefab inside a resource folder called enemy and you want to instantiate it.

var instance : GameObject = Instantiate(Resources.Load("enemy"));

you can create asset bundles of your prefabs and put them inside your game folder too. then call www("file:/path") and get a reference to them and instantiate them. there is another way too. you can create a class that keeps a list of all prefabs in a dictionary. the name of those prefabs in the dictionary could be your key and the real GameObject reference could be the value.

Slight update to Ashkan's totally correct answer (this time in C#)

Create a folder called "Resources"

GameObject monster = (GameObject)Instantiate(Resources.Load("enemy"));