On my G4 1.5 gHz early model (BT 1.1), the CPU had thermal compound which was black and stiff. The system controller had what appears to be a thermal pad on the heat sink, and the GPU had a gray colored sticky putty-like compound, which I assume is silicone-based thermal paste. When I removed and replaced the logic board, I scraped off all the black stuff from the CPU die and copper heat sink, cleaned both with 91% isopropyl alcohol, and applied Arctic Silver 5 thermal paste to the CPU die and GPU surfaces. I am not sure if the GPU needs the thick silicone paste or not -- time will tell I suppose.
Look at
this image for relative locations of the components. From left to right is the CPU, controller, and GPU.