Intel CPU and Surface Mounted Capacitors (located directly on top)
These are the regular power bypass capacitors. The distance from the die to bottom pads is substantial, so the inductance of nets is substantial too. The CPU has multitude of rails with dynamically changing power consumption. The caps are there to eliminate/reduce current starvation on spikes of consumption. 
If the caps are placed only on mainboard, plastic substrate lead/plane inductance will not be able to supply changing current, and voltage will drop killing CPU functionality. That's why the caps are placed as close as possible to the die.