3. Egypt Air flight 990
It was a regular flight from Los Angeles to Cairo, with a stopover at JFK airport, New York.
The plane crashed into the Atlantic Ocean on 31 October 1999.
The accident killed 217 people.
The Egyptian government reversed the decision of the American National Transportation Safety Board that the incident was intentional and not an accident.
The two investigations came to very different conclusions: the NTSB found the crash was caused by deliberate action of the Relief First Officer Gameel Al-Batouti; the ECAA found the crash was caused by mechanical failure of the airplane's elevator control system.
It still remains a mystery as to what caused the crash.
4. British South American Airways Star Dust
Star Dust (registration G-AGWH) was a British South American Airways (BSAA) Avro Lancastrian airliner which crashed into Mount Tupungato in the Argentine Andes on 2 August 1947, during a flight from Buenos Aires to Santiago, Chile.
After the search operations were called off, many conspiracy theories cropped up. So the case was put to rest.
After 50 years, when mountaineers while trekking discovered the remnants of the air plane crash, it was declared that the plane had crashed due to weather related factors.