According to the Shulchan Aruch, someone traveling in a ship and unable to stand may pray while sitting, but must pray over again when he reaches his destination. (Today, however, due to our low level of concentration during prayer, we wouldn’t daven over, but rather would rely on the sit-down tefilla.)
On a ‘jumbo jet’, though, there are places where ten or more can stand and daven together, while following common courtesy: Pray quietly, avoid stepping on toes, don’t block the bathroom or aisle, etc.
To find out El Al’s official policy towards in-flight prayer groups, I called their assistant director of public relations. The official told me, “El Al is a Jewish airline. We have never stopped this [people davening with a minyan] … We do know that people are complaining about this.” If enough people were to congregate and cause a noticeable weight imbalance, the captain would be obligated by international aviation regulations to disperse them, said the official, but this never actually happens.
I asked Rabbi Chaim Pinchas Scheinberg, shlita, if one should pray with a minyan on an airplane. He said yes, adding that he does it “all the time.” While strictly speaking it might be permitted to pray at your seat, Rabbi Scheinberg prefers that one pray with a minyan, but quietly in a way that doesn’t disturb others.
* Shulchan Aruch Orach Chaim 94:4,9 article from Ohr Somayach’s site