The Iron Nugget currently has no use in Tekkit, but can be crafted into Iron Ingots by filling the crafting space. Nine Iron Nuggets can be crafted from one iron ingot and can used as a form of currency in many servers. A Gold Nugget functions in the same manner.
It also can be used to store iron, although iron blocks are much more purposeful to do this, but requires more iron. This is also very inefficient, but useful for PVP servers- they have to get back with the nuggets to actually do something with it.