RIght now Intel chips run hotter than AMD chips. This wasn't the case a few years ago - AMD has developed a stigma of being hot chips that will be hard to distance themselves from.
The main contributor to thermal dissipation is voltage, feature size (through voltage) and speed. There are two types of heat dissipation in chips:
1. Each time a trasnisitor changes state (from 1 to 0) a certain amount of heat is dissipated - this is called active power. The active power is dependent on the voltage to the chip, and the voltage of the chip is determined by the size of the average feature on the chip. The active power dissipated by the chip is a function of the dissipation of a single transistor times the number of times the transistor changes state per second. Hence, higher speeds means more heat produced.
2. THe second type of heat dissipated is leakage current. Leakage current is power that flows in the chip when transistors are not switching, ie. energy that is not used to perform calculations. Leakage current increases with voltage and increases with decresing feature size. At higher voltages, there is more potential for current flow across a closed gate. At smaller feature size the oxide layer is smaller and there is less electrical resistance to current flow across a closed gate.
If you're looking for more details you'll have to ask an Electrical engineer - I'm not sure I have a full grasp of the quantum physics involved with transistor switching.
Edit: CPUs get hot because they produce a lot of energy. Energy dissipation from one object to another is proportional to the difference in temperature between the two objects. So a CPU will accumulate energy (heat up) until the temperature difference between the CPU and the ambient air is sufficient to dissipate the same amount of heat that a CPU produces.
Q = heat dissipation
A = Area
deltaT = Temperature Difference= Tcpu-Tambient
U = heat Trasnfer coefficient
Q=UA(deltaT)
So to increase heat trasnfer, you either have to increase your area (larger heatsink), increase your heat trasnfer coefficient (watercooling, phase change cooling or higher clamping pressures for heatsinks) or higher temperatures to increase the temperature differential.
I may not be able to answer EE type questions, but I'm alright with heat transfer. If anyone wants more details, just ask.