Тройная вложенность

SELECT * FROM flights, airport, city
  WHERE flights.fromAirport = airport.code AND flights.toAirport = airport.code
  ORDER BY flights.upload DESC
  LIMIT 1;

SELECT f.flightNumber, cF.name townFrom, cT.name townTo
FROM flight f, airport aF, airport aT, city cF, city cT
WHERE f.fromAirport = aF.code 
  AND aF.cityCode = cF.code
  AND f.toAirport = aT.code 
  AND aT.cityCode = cT.code
-- AND f.flightNumber IN (123,456,789)

Вариант с использованием конструкции JOIN:

SELECT f.code, cf.name AS fromCity, ct.name AS toCity FROM flight f
    INNER JOIN airport afrom ON f.fromAirport = afrom.code
    INNER JOIN airport ato ON f.toAirport = ato.code
    INNER JOIN city cf ON afrom.cityCode = cf.code
    INNER JOIN city ct ON ato.cityCode = ct.code
ORDER BY f.code;

А вот и рабочий пример на SQLFiddle.

У вас должно быть примерно так:

SELECT name  FROM city 
JOIN airport ON city.code=airport.cityCode
JOIN flights ON airport.code=flights.fromAirport
WHERE flights.fromAirport=12345