From the manual the blinking red light indicates too high internal temperature. The suggestion to power down and let the console cool down does not always have the desired effect. Obviously then the cause is not too high internal temperature (at least not at the moment.)
First, it is called the "Yellow Light of Death" because the console briefly lights up both the red and green LEDs, mixing them into a yellow hue. There are actually many causes for the YLOD, because it is simply a way to signal that some unrecoverable error was discovered by the system controller. The system controller is responsible for the start up of the system, and it monitors the process for errors. If an error is detected, the system is shutdown with the YLOD syndrome.
One of causes could be that one or both of the Cell Broadband Engine or the RSX Reality Synthesizer graphics chip have become hot enough to adversely affect the solder balls of the BGA chips.
Since Sony is bound to follow the RoHS directive, it's likely that they use lead-free solder balls. Lead-free solder has a higher melting temperature but it is also more prone to become brittle due to effects of temperature. It's not necessary for the solder to become hot enough to actually melt to be affected.
When the PCB is heated by the chips, it will tend to deform and warp. If the solder is hot enough, it can experience a cold solder joint that will break the connection between the ball and the motherboard.
Now, some people have contended that Sony's use of a ceramique based thermal paste is the reason for these YLODs. Or that they have used too much paste.
I say this is unlikely. The temperature difference between the different types of thermal pastes are a couple of degrees. Such a small difference is not likely to have such an adverse effect on the solder.
However, what's with the big blob of thermal paste?
To one of my motherboards, I decided to apply a very, very thin layer of Arctic Silver 5 thermal paste, thinking I would improve the heat transfer.
However, after turning on the PS3, loading up a game, suddenly the PS3 would quickly overheat and die with the YLOD! The effect was only temporary and following Sony's advice, letting it cool down allowed it to be powered on again, although the overheating would repeat itself.
After disassembling once again, the cause for this behaviour was very apparent:

This is of course certainly not enough to lead away enough heat! Why did this happen? Let's have a look at the original paste from the console:

Why did I get such a poor connection? It wasn't a fluke either, I tried to reapply thermal paste two times, each with similar results! Maybe the heatspreader/heatsink is a bit deformed and require a thicker layer of paste. Also, I might not have tighten the screws enough. It's important to really pull them as tight as possible, although be careful not to damage the screw heads.
Also, the heat sink only uses two pins to connect it with the heat spreader. On a computer heat sink, there are usually four pins.
I will post more about the YLOD and my experiences with it later!
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