I've used small nails myself. Once I've cut off the limb, I then hammer a nail into the where I want the joint to be, once the limb is on the nail, trim the nail using a wire cutter (otherwise you get the pointy end sticking out of the figure) and then hammer the nail and limb to the body.
Of course this is only good for rotating joints like arms or legs. Howeve if the nail is too short, the limb might fall out, too long and it can poke out the other side.
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Nibelilt: I suggest finding spare parts at your local thrift store. My local "Volunteers of Ameica" sells me bags of toys for 90 cents. Transformers, star wars, etc. Usually they are the right type of joints for customs like this.
Buzzthebatgirl: why nails? I'd think a screw would stay in better.
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