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1. Where did the water come from for the flood, and where did it go?
The oceans contain more than enough water to flood the Earth. If Earth's surface were perfectly smooth, with no mountains or ocean basins, it would be covered by a layer of water 3 km deep.  Before the flood, some water was probably in the seas, some in the atmosphere, and an unknown amount of water may have been underground. Most of the surface water is now in the ocean basins, but there may be even more water in the mantle.  It is possible that more water was added during the flood by collisions of one or more comets, which appear to be made largely of water. 
2. How could the waters of the flood cover Mt. Everest?
The topography of the land today is not the same as it was before the Genesis Flood. It is likely the entire crust of the earth was reorganized during the Flood, as the original surface was eroded away and the sediments deposited in basins. Many organisms were also transported into these basins and subsequently buried, thus forming fossils. During the flood, the area that is now Mt. Everest was a basin in which sediments were accumulating. This is shown by the presence of marine fossils on Mt. Everest.  After the deposition of the fossil-bearing strata, tectonic activity raised the sediments high above their previous position, forming the Himalaya Mountains. Most or all of our present mountains may have been formed similarly by tectonic activity during the Flood or shortly thereafter.
3. How could the Earth be destroyed by 40 days and 40 nights of rain?
That is not all that happened during the flood. The flood waters apparently did not begin to drain for some 150 days (Genesis 7:24). Another 150 days seems to have passed before the ark landed (Genesis 8:3,4). Ten months of continuous flooding would probably produce major geologic changes in Earth's surface. In regions away from where the ark landed, the flood might have lasted considerably longer than one year. Rain was an important factor, but there was much more than rain involved in the global catastrophe known as the Flood. Strong oceanic currents would be formed when the former land surface was submerged. Large masses of rocks and sediments were transported and re-deposited at a distance by turbidity currents and submarine landslides. The rock layers show many folds and faults, indicating large movements of portions of the crust, associated with plate tectonic activity. In addition, the rock layers contain more than 150 craters formed from impacts of extraterrestrial objects such as asteroids, meteorites and comets.  Volcanic activity is another factor that disrupted the earth’s crust. Enormous lava flows, called flood basalts, are found in several places in the earth’s crust. Volcanic eruptions and lava flows would have released gases, ash and magma that covered large areas of the earth’s surface. These processes would have multiplied the effects of the water, and the Earth's crust may have undergone a major rearrangement during the flood. 
4. Was the flood truly worldwide?
The wording of the biblical text consistently points to a global flood.  Jesus used the Flood as an example of universal judgment (Matthew 24:37-38). Peter confirms that only eight people were saved (2 Peter 2:5). In the Genesis text, the language is as universal as it is possible to be: "... all the high mountains under the whole heaven were covered" (Genesis 7:19, RSV). If water covered the high mountains it would also cover the lower regions. Since it was God's purpose to destroy all humans (Genesis 6:7), the flood must necessarily have extended at least to all regions inhabited by humans. Furthermore, God promised there would never be another flood like that one (Genesis 9:11, Isaiah 54:9), as symbolized by the rainbow (Genesis 9:13-17). There have been many highly destructive local floods that wiped out many people. The rainbow is seen worldwide, indicating the promise applies worldwide. The Genesis flood had to involve a different level of activity than anything seen since that time.
5. What about proposals that the biblical Flood story refers to a local flood somewhere in the Middle East?
None of the proposed local floods fits the biblical description. If the flood were local, the biblical flood story wouldn't make sense. There would have been no need for an ark to save Noah or his animals. Noah could have migrated with his animals to another region to avoid a local flood. Some have pointed to a layer of clay in some parts of the Mesopotamian Valley as the source of the biblical flood story.  However, this clay layer is found in only some of the cities in the area. Undoubtedly, the region has been flooded on occasion, but this has nothing to do with the Genesis flood of Noah. Another proposal is that the biblical flood story is based on the re-flooding of the Persian Gulf due to rising sea levels as the glaciers melted at the end of the Ice Age.  Another great flood in the Black Sea has been claimed as the source of the biblical flood.  These reports may refer to actual floods, but they do not fit the biblical story, in part because these “floods” have not ended, in contradistinction to the biblical story. Several other major prehistoric floods have occurred that appear to have exceeded anything in recorded history. The Channeled Scablands Flood in the State of Washington is one such example  but several other examples have been described.  None of these fits the biblical description of the flood as a global event that destroyed all humans except the eight in the ark.
6. What unsolved questions about the Flood are of greatest interest?
How did the flood produce the fossil sequence? How did the plants and animals reach their present locations after the flood?
 Dubach HW, Taber RW. 1968. Questions About the Oceans. Publication G13. Washington DC: U.S. Naval Oceanographic Office, p 35.
 The mantle is capable of storing more water than now exists on the surface: Murakami, M. et al. Water in Earth’s lower mantle. Science 295(2002):1885-1887.
 See Hartogh, P et al. Ocean-like water in the Jupiter-family comet 103P/Hartley2. Nature 478(2011):218-220.
 Odell NE. 1967. The highest fossils in the world. Geological Magazine 104(1):73-74.
 To date, 184 confirmed impact craters have been identified; see http://www.passc.net/EarthImpactDatabase/Diametersort.html, accessed 1 October 2013.
 A theory proposing this is described in Austin, SA, Baumgardner, JR, Snelling, AA, Vardiman, L and Wise, KP, Catastrophic plate tectonics: A global flood model of Earth history, in Proceedings of the Third International Conference on Creationism, RE Walsh (ed), 609-621.
 Hasel GF. 1975. The biblical view of the extent of the flood. Origins 2:77-95; Hasel GF. 1978. Some issues regarding the nature and universality of the Genesis flood narrative. Origins 5:83-98; Davidson RM. 1995. Biblical evidence for the universality of the Genesis Flood. Origins 22:58-73.
 E.g., see Woolley, L. Stories of the creation and the flood, in (A Dundes, ed.) The Flood Myth. Berkeley: University of California Press (1988): 88-99
 Rose, JR. New light on human prehistory in the Arabo-Persian Gulf oasis. Current Anthropology 51(2010):849-883.
 Ryan, W and W Pitman. Noah’s Flood. New York, NY: Touchstone, 2000.
 See Allen JE, Burns M, Sargent SC. 1986. Cataclysms on the Columbia. Portland OR: Timber Press.
 A great Siberian flood is described in: Baker VR, Benito G, Rudoy AN. 1993. Paleohydrology of Late Pleistocene superflooding, Altay Mountains, Siberia. Science 259:348-350. Hsu KJ. 1983. The Mediterranean Was a Desert. Princeton, NJ: Princeton University Press; Gupta, S et al. Catastrophic flooding origin of shelf valley systems in the English Channel. Nature 448(2007):342-345.