well.. I havent taken thermodynamics yet.. but what about the transfer of heat to the mug itself? ceramic is a GREAT insulator and will only absorb a small amount of heat from the water... but that change in temperature will GREATLY affect the resonance of the sound generated on the ceramic... maybe thats why you get a lower tone? the ceramic is more flexiable and makes a duller noise than when the cold water splashes into the cup and makes a very obvious splashing noise...
maybe we should check the sounds different temperatures of water make in different material cups
