I know that a ship is always referred using "she", but what about aircraft? What should we use when we're referring to aircraft? Is it the same for automobile?
The most common way to refer to an airplane is it.
If one were to decide to infer gender onto an aircraft, female would be the obvious choice for airships (eg Zeppelins), and by extension probably the logical one for smaller aircraft like planes.
However, I would advise against doing any such silly thing. Getting rid of gender for inanimate objects is one of the main features of English I like.
For automobiles, there really isn't a standard. The most common usage is again "it". My mom had an odd tendency to name her cars, but they were generally neutral names like: "The Blue Blump". Probably the most popular personified cars in media are Herbie the Love Bug (male), Christine (female), and the Cars cartoon series (both).
As a pilot, the aircraft is definitely a she. Look after her, keep her in balance and she'll reward you; she'll work with you to get you there smoothly and comfortably and she'll becomes an extension of your hands.
Each aircraft has a personality of her own; it's easy to personify different idiosyncrasies as different personality types. A slight miss on throttle-forward might be an emphasyemic cough, an out-of-balance rudder might be a wooden leg; these things become what you love in an a/c.
If an aircraft is given a gender, it is normally female, along the same lines as for ships and for much the same reasons (complex creatures with very fickle attitudes toward their men, that are nonetheless objects of affection).
The anthropomorphism of aircraft is rarer than for ships, but still very common especially in the military, where bombers and even fighter aircraft have traditionally been given a name and "nose art" for good luck (more commonly as simply something for the lonely pilots and ground crew to ogle). The bigger the plane, the more likely it is to be anthropomorphized. Race cars are also anthropomorphized by their drivers from time to time.
As I read the question: 'WHAT IS the gender of an aircraft? What should we use when we're referring to aircraft?...', NOT, '...the question was basically whether one should refer to an aircraft as "she" as we do a ship...'. To continue, I think 'nose art' had a lot to do with it during WWII, where 'airships' often had female artwork (and attendant names) directly under the pilot's side of the fuselage as an 'affectionate' anthropomorphism to remind the crew of females they'd left behind, dreamed of, or had the characteristics of women within a plane's often sensitive controls during take-off, cruise and landing. Having said that, there were also not a few aircraft with male (often chauvinistic, comical or downright dirty) artwork and names (depending on their necessarily rigorous maneuverability). Still, I think it comes back to the finesse of the 'delicate handling' of aircraft. They are sensitive to the touch, respond with only a modicum of manipulation during flight, and with just the right amount of direction, bring her crew and passengers into a comfortable repose whether her '_heels' are lifted-up or placed gently on the ground after an exhilarating trip - alleviating pent-up stress and with a great deal of satisfaction. ~N'est ce pas?