I always cover the rear mech with a plastic bottle (like others on here), drop the saddle, drop the bars and turn 90 degs, remove the pedals, deflate the tyres & remove the wheels, fit spacers to the forks and rear stays, then cover all frame tubes in foam pipe lagging (bought from plumber's merchants, B&Q, etc...comes in different sizes). Drinks bottles are left in the cages on the bike. Then I put the lot into a Bioracer bike bag, which holds the wheels either side of the frame. Also in the bag is my track pump and toolkit. I mark the bag as Fragile.
Before you start to dismantle anything, mark a line with a marker pen so that you know exactly your position. Nothing worse than playing around with your setup at the other end when you could be training/racing. It takes 5 mins to put everything back together at the other end.
I used the above method to fly to Germany, Switzerland, Ireland, Canada, Cyprus, Ascension and the Falklands without any mishaps whatsoever.