From the top of my head:

- Charles Nungesser and François Coli over the Atlantic in 1927;

- The Italia airship over the North Pole in 1928 (the envelope disappearing together with some crew after it crashed and the control cab broke off - some survivors from the control cab were rescued)

- Charles Kingford Smith in 1935;

- Amelia Earhart and Fred Noonan in 1937;

- Flight 19 and one of the PBM Mariner search aircraft (1945);

- The Airborne Transport DC-3 that disappeared somewhere between Puerto Rico and Miami in 1948;

- The Air France Latécoère 631 that disappeared in 1948;

- Star Tiger and Star Ariel, two Avro Tudor airliners of British South American Airways that went missing off Bermuda in 1948 and 1949 respectively;

- The USAF Skymaster that disappeared over Canada in 1950;

- The Skyways Avro York that disappeared over the Atlantic in 1953;

- The Pan American Boeing Stratocruiser, that disappeared midway between Hawaii and San Francisco in 1957;

- The KLM Super Constellation that disappeared about an hour into its flight from Shannon to New York in 1958;

- The Artop PBM Mariner that disappeared between Lisbon and Funchal in 1958, barely a month after the airline had started flying;

- The Flying Tiger Line Super Constellation that disappeared over the Pacific in 1962 (one of two Flying Tiger Line Super Connies to encounter an accident on the same day, IIRC they even took off from the same airport...)

- The Boeing 307 Stratoliner that disappeared over Vietnam in 1965;

- The Cessna 310 carrying two politicians in Alaska in 1972;

- The Varig Boeing 707 freighter carrying a load of paintings that disappeared over the Pacific off Tokyo in 1979;

- The German Learjet enroute from Vienna to Hamburg that suddenly went silent and off-course in 1983, only to run out of fuel over the Atlantic somewhere between Scotland and Iceland (although its crash was witnessed by two USAF F-15s scrambled out of Keflavik)

- The Boeing 727 that was stolen out of Angola's Luanda airport in 2003, presumably by a single pilot;

And I'm pretty sure there are many, many more that I've forgotten about, especially smaller aircraft.