What you will need:
Multi-tool
Pedal wrench (will vary depending on your pedal)
Pipe insulation (can get this at Home Depot. Get a couple sizes of 6 foot long strips)
Long zip ties
Scissors
Bike box (I use a Serfas and it is just fine. Your LBS probably sells used ones)
Plastic thingamabobs for your wheel axle and bike frame (comes with box)
Masking tape (blue painters tape is ideal)
Ziploc bag

Step 1: The F&%%#ing pedals!
This is by far the most frustrating part of the whole experience. A pedal that has been on for a long time can be a serious pain to get off. Twice I have just taken my bike to the LBS to have them take them off. (I have never been charged for this) But with the proper tool you should be able to do it.
!Important! Pedals are designed so that they will not loosen by riding. Subsequently they are threaded in opposite directions. The right pedal is a normal thread. Lefty loosey applies. The left pedal is threaded opposite. So in order to remove it you have to turn it to the right
Non-drive side (finger pointing in direction of loosening:

Drive side- again, finger pointing in direction of loosening

KEEP IN MIND: If you have Look pedals they remove from the inside using a Hex wrench. Buy a long one with a handle- you will need leverage. Pictured above I am using my multitool. This will work if your pedals have been removed recently and/or tightened by hand. Don't let the fact that you are unscrewing from the inside of the pedal confuse you. Just look at the above pictures for the correct direction.
If you have a trainer, remove the pedals when it's on the trainer. It will help stabilize the bike if you need to put extra torque on the tool.
When pedals are removed, put the pedals and washers into the ziplock bag
Step 2: Remove seat
Remove the whole seatpost. There should just be 1 or 2 screws to loosen on the frame. Loosen by a few turns and lift the whole seatpost out of the frame. Set aside.
Loosen the screw on the "collar"

Pull seatpost straight out:

Step 3: Remove Headset
There are 2 parts to this. There are 2 screws on the side which tighten the headset down, and then one long screw that goes through the spacers into the fork. Take the long screw all the way out and put the screw and any spacers you have on top of the headset into the ziploc.


Loosen the 2 on the side. Don't take the headset off yet.
These are the 2 screws I'm talking about:

Step 4: Take off your wheels.
If you have a rear wheel drop out make sure your chain is in the big ring up front and smallest ring in the back. This will make it easier on you. Remove the skewers first and put in the ziploc.

Take off the wheels and set aside. Place frame in the bike box on top of one layer of padding (put the other 2 layers aside), drive side up.

Step 5: Pull off the headset and put any spacers from under the headset into the ziploc.

Tape the brake levers down.

Step 6: Remove your rear derailleur. DO NOT FORGET THIS STEP. A bent derailleur hanger is a ruined frame. It is just held on by a single hex screw. Completely unscrew the derailleur and remove from hanger. Tape it down to the frame when you are done. Don't worry, it just screws right back on when you get to your destination- no adjustment necessary (I will do another post on putting a bike back together)


Step 7: PADDING!
Cut pieces of pipe insulation to fit on each piece of your bike. Pipe insulation is great because it has a slit and you can pop it right over your frame. Secure each piece with a zip tie. I use 2 pieces together to cover my downtube since it is a wide aero tube.

Step 8: Put on the plastic frame protectors where your wheels should be. These should come with the bike box.

Step 9: Put the multi-tool into the ziploc bag. All the necessary parts to put the bike back together are now in the bag. Close the bag and tape it to the side of the box so it can't roll around and hurt your frame.

Step 10: Tape your seatpost and handlebars to your bike. Put your helmet and water bottles in the box. That's all I will put in my box because of weight, and also because anything heavy could damage the frame if it comes loose. Make sure your fork is oriented as shown in the pic:

Step 11: Cover the bike with insulation piece #2

Step 12: Put plastic protectors on the wheels. This prevents the axles from going through your frame

Step 13: Lay down the wheels, overlapping in the box. Put an old shirt between them where they rub. Make sure the wheel axles are not directly over a piece of your frame

Step 14: Put the third piece of insulation over the wheels

Step 15: Put the top of the bike box on. It should be tight. This is what keeps things from rattling around.

Main principles:
Tape everything to the frame or to the box. Your box is likely going to be opened. You want TSA to be able to life your bike out of the box and not disturb any of your hard work. If everything is taped together, it can't be screwed up when it is put back in by a non-bike person
Don't put a bunch of crap in there. It just increases your likelihood of scratching your frame and being overweight. Staying under 50 pounds is the key to not being doubly charged at the airport. The only other things I put in the box are my water bottles and helmet.
Don't lock your box without a TSA approved lock. TSA will just cut it.
Once you've done it a couple times it will only take you 10-15 minutes to pack and unpack. Give yourself plenty of time the first time. ALWAYS make sure that you can loosen your pedals on your own a couple days before your plane leaves. You need to give yourself enough time to get to a bike shop if you need assistance or don't have the right tool.
That's it! Let me know if I've missed anything. I hope this helps someone!