thermal analysis pcb
I am not familiar with the commercial tools (I think they are too expensive), but I have some success with ThSim (from sourceforge.net). This program translates the heat generation/distribution network to an electrical RC equivalent and then uses Spice for simulating this, then reads back this data and displays the heat dissipation in the structure.
The basic inputs that you need are: material properties (size, thickness, thermal conductivity, specific heat capacitance, specific weight) and the generated power.