Malta Direct (the holiday division of Air Malta) have always been cheapest whenever I have looked into fares. Occasionally there are last-minute deals on some of the travel website - bargainholidays.com, lastminute.com etc., but they tend to be complete packages rather than just flights.
It is possible to travel to Malta by ferry from Italy, so it could be cheaper to get a no-frills flight to Italy and catch a boat, but it would probably be a complete nightmare to organise!