Like I said earlier, a bomb, maybe. A missile, NO. Take away all the "eyewitnesses" and the missile theory goes poof! I have yet to read an eyewitness account of any airliner crash where they get more than a small amount of the facts straight. Also, these people were not anywhere near the actual crash. They were miles away seeing an event that at the time they had no idea what it was. Even when eyewitnesses are within spitting distance of a crash, (AA 587) they cannot agree on what actually happened.
The so called "facts" of the missile theory are great, as long as the facts that rule out a missile are ignored. The problem with conspiracy theories, is one can be created to fit any event. If it was a U.S. Navy ship, it would be impossible to keep the entire crew quiet for all these years. Someone would leak it to the press that their ship fired a SAM at the same time TWA800 went down. Also, there were not any SAM equipped ships within range of TWA800 unless we have a secret, ship launched version of the Phoenix missile.