Yes, there is evidence of a great flood in ancient times. However, the evidence is not paleontological (the fossil record). The evidence is geological, with additional archeological evidence as well.
The best evidence points to the loss of a land mass separating the Mediterranean Sea and what is now the Black Sea. This probably occurred near the end of the last ice age, some 10,000 years ago. As the ice caps melted back towards the poles, sea level rose and the 'plug' at the mouth of the Black Sea was either undermined or overtopped (or both).
As we saw in the Tsunami disaster last year, huge amounts of water rushing over a land mass causes catastrophic damage. Imagine the December 2004 tsunami, raised to the power of 100. The geologic and hydraulic evidence suggests that the water may have rushed as far inland as Kazakhstan.
There is additional evidence of land mass loss at Gibraltar, caused by the rapid draining of the Mediterranean and a subsequent change in hydraulic pressure. This would have resulted in a second, even more catastrophic Tsunami, as water from the Atlantic rushed through the Mediterranean Basin. It would have certainly flooded most of the ancient world.
It would certainly also have changed regional weather patterns, and it's entirely likely that heavy rainfall would have occurred over the region.
However, there is no evidence that China, Japan, South America, North America or sub-Saharan Africa were flooded. All of these continents were inhabited by the end of the last Ice Age, and civilization had been well under way in most of them.
Did the whole world flood? Well, if you lived in the middle east, it would have seemed like it.