I didn't get a chance to read through all the previous responses but figured I'd chime in. I know of two ways to make a very similar problem happen. The first is excessively high idle speed adjustment, and when the brake pedal is stepped on, the surging begins. If the brake is released, the surging goes away. The second way I know of to make this happen is low coolant or an air bubble. I routinely have this surging happen after I've flushed coolant or installed a new engine and I'm waiting for the engine to warm up and the t-stat to open. Now, while neither of these issues may directly be related to your problem, they may help. If there's an air bubble at the engine temp sensor, it will cause the surging. Have you checked or replaced your temp sensor? Second, the computer knows the brakes are applied and cuts the injectors until the RPM's drop down (below around 1300RPM). The theory is that if you are braking, you are not stepping on the gas and don't need fuel. There's a basic switch on the brake pedal assembly that's responsible for turning the tailight's brake light bulbs on, but the wire does not run straight from the pedal to the bulbs. The wire goes through the computer, and that's how it knows the brakes are applied.
So, a few thoughts that come to mind are 1) malfunctioning computer, 2) improperly adjusted brake pedal switch 3) malfunctioning temp sensor.
Whatever the issue is, it appears to be an all or nothing deal. Meaning, it's not just affecting one cylinder such as would be the case with a bad wire or plug. It's affecting everything, and it's symptoms are very similar to an air bubble at the temp sensor or high idle.