More than likely, as Nahemoth stated, 'memento mori'. A thought to the finality of all. I personally have a wolf skull placed on my altar... They are very aesthetically pleasing to some folk, and a good way to channel and focus Will/Energy for destruction rituals.
I'd imagine the CoS uses such a skull for the aesthetic psycho-dramatic bend of it. Though I have heard that lately the use of a white candle set atop a skull has replaced the standard white candle used for burning writings during ritual, so both my above statements could be valid. In hindsight, I suppose they are pretty much interchangeable.