I think TWA-800 needs to be re examined. Micheal Leeden makes the point that all bureaucracies tend to accept the explanation that they are most comfortable with. The FAA, FBI and CIA did not want to believe that a missile brought down an aircraft near the coast of the United States.
There were also serious economic considerations. Imagine what would have happened to commercial aviation if it were revealed that a surface missile shot down TWA 800. The impact of 9/11 would have paled in comparison if air travelers believed that they risked being shot out of the air by some terrorist with a hand held missile. There must have been tremendous political pressure to come up with the "right" conclusion.
It always makes me suspicious when the FBI does a plane crash investigation instead of the NTSB, and when they rule out terrorism in the first press release.