You would form a closed circuit out of the batteries. In situations like this you have to take into consideration the internal resistance of the batteries. Think of the batteries as a voltage source in series with a resistance. The resistance depends on the type of battery e.g. quite high for zinc carbon, very low for NiCd.
Joining two batteries of different voltages would cause a current to flow between the batteries as follows.. I = (Vbatt2 - Vbatt1) / (Rbatt1+Rbatt2)
i.e. your batteries will probably get hot.
Its a waste of batteries and probably dangerous if you use batteries of low resistance like rechargeable.
akg is right that in the end the higher voltage battery will discharge into the lower one, until they are both at the same level, but this could take some time if the internal resistance is high, or it could be near instant (hopefully not as this would probably cause your lower voltage battery to burn up / explode)