Why anyone uses WD40 as a cleaning agent is beyond me. It's a lubricant and moisture repellent (in fact, the WD stands for "water displacement"). The fact that it's reacting with some parts is reason enough to drop the habit.
Anyway, take apart, scrub with toothbrush and household cleaner of choice.
WD40 was developed primarily for water displacement in rockets/planes, to prevent ice formations, hence all connections in the circuitry are solder-less. It took them 39 tries to get the solvent just right, and on the 40th attempt, they did so, and Water Displacement 40th Formula (WD40) was "born". The fact that WD40 can be used as a lubricant is just a by-product, which its marketing relies only heavily today.
I never specifically said to use WD40 to clean the controllers. I said use WD40 to bring back its "like new" shine (in less words), only once he has cleaned the controller with warm water, washing up liquid, and a tooth brush. The only reason why I told him not to use WD40 on PS3 controllers (or any controller that is semi-transparent) because they are made with polycarbonate plastic. If you read WD40's FaQ, it will tell you;
Polycarbonate and clear polystyrene plastic are among the few surfaces on which to avoid using a petroleum-based product like WD-40.
There is another product out there that gives just as good results, but I can't remember the name off of the top of my head (will take a look for it later).
Here's a video to give you a brief idea of what I actually meant.
http://www.youtube.com/watch?v=XF3S8oredDkEDIT: Also, like Isopropyl Alcohol, WD40 is made with a solvent which has low conductivity, so using it to clean metal contacts, as suggested by the WD40 FaQ, is fine. The solvent WD40 is a petroleum based solvent.