Hi guys, I second the opinion that the pi-bluetooth service or ps3 service are at fault. I connected one of the controllers through the USB cable and the emulators have run for 4 hours straight with no problems. I tested Mario Kart for n64, TOCA2, Final Fantasy VII, Tekken 3 and Carmageddon for PSX and there was no problem, even though in the past my system froze in each and every one of those games.
To finish the test I exited the emulators and tried to connect the second controller via Bluetooth. The controller didn´t even have time to pair and emulatorstation froze. I guess I´m stuck with wired controllers for now, but I´d still try to get to the root of the problem.
Could there be a communication problem between the PS3 wireless service and the bluetooth service? I have yet to find other posts on the internet complaining that bluetooth on the rPi froze the system.