I've had friends with exactly the same problem: runs rough after the car was parked through a heavy rain. Runs fine after a while. Problem doesn't sho up again, until it's parked through another heavy rain.

If this is your symptom, it may be time to replace your spark plug wires. Once the wires get worn out, they tend to collect moisture. The heat of the engine will dry them out, so that's why the car might not show this problem when you drive it in the rain. But when you park it in the wet, moisture collects, and the car runs like shit (until the wires dry out again).

Thanks,
Eric