When smelting Ores (not dusts or processed materials) You will receive a nugget for that ore. This also works on meat (cooking chicken will give chicken nuggets)
I'm not sure on the chance but I believe its around 25%, but when you add all of the arcane bellows to it that you can(one on each hole on the side), it not only becomes faster and uses less aura, it also increases the reward chance to something like 90%.
One thing I should mention is although the description says its "free" it's far from it (in Thaumcraft 3 anyway. in Thaumcraft 4 it is free, as explained in the comment). it uses aura from the atmosphere in order to smelt, so if you are using it as a primary furnace and smelting a lot. I suggest getting some aura generation items around otherwise that area will become a painful area.