Getting the boat ready for shipping involves mainly taking things apart and tying them down. Here is my rough check list:

When the boat is in the water:
1) remove solar panels from Bimini, and stow below
2) Remove Dodger and bimini panels
3) Remove main and Genoa, stowing battens and poles for mainsail cover in the boom all taped together
4) Remove mainsail cover
5) Go up the mast and remove windex, wind wand and SSB Antenna
6) Remove vang
7) Pull all halyards and reef lines etc, back to base of mast, and out of mast base turning blocks
8) Disconnect in mast wiring and tape to side of mast
9) Wind genoa roller furling line completely into the drum so it is not attached to the boat
10) Wrap the reef line ends around each end of the boom to pad it, remove mainsheet blocks and mainsheet from boom, and then remove the boom, placing it on the side deck
11) At this point, the mast should be completely free from the deck except for the shrouds
12) Remove Chute tack line/downhaul
13) Take out shroud cotter pins and loosen the rig some.
14) Pull the mast, put mast wires inside mast (remove from exit hole) so they can not be smashed as the boom is moved in the yard.
15) This is also a good time to service the engine and if you are shipping to a cold climate, winterize everything.
16) Tape Solar and SSB wires to stern pulpit

Now it is time to haul the boat.
1) Step back and watch!

To prep the mast: (The specifics are based on the Beneteau 46 mast design, but the steps are generally applicable to any boat.)

1) Remove lower shrouds, and roll into a bundle using tie wraps
2) Remove cap from upper spreader end to take the upper shroud wire out of the spreader end, creating some slack.
3) Remove the lower spreader end caps with the shrouds attached (Push spreader upwards to give you some slack to wiggle it free of spreader tube), disconnect the middles and uppers from mast. Roll the assembly into a coil and tie wrap it, marking the sides so you know which is port and Starboard for re-assembly.
4) Remove and coil backstay
5) Remove lazy jacks and running backstays, and using a messenger line, remove each halyard. Good time to end for end them by putting the shackles on the other end once pulled. Stow the halyards in boat. They make good packing for anything you don't want to shift, I stow them under the cabin floor boards.
6) Remove the spreaders, leaving bar in place with bolts taped in the bar so it can not move and bolts don't go missing. Clean and wrap the spreaders together, as two sets. Pad the ends and stow below in aft cabin.
7) Remove headstay pin and slide headstay up mast so drum is near mast end. Move it towards the back side of the mast. Put it tight along the mast, pad it every three feet with water pipe foam, and tie it tightly to the spreader based and any other good tie point. Tape it where there is no good tie points so it can not move. Try to use foam that does not have a sticky edge, this only creates a mess when used for padding. Tie wraps or small rope seem to work well. The shrink wrap tape was a pain to remove and in spots left a residue, so use it as little as possible.
8) Remove the sail feeder, slide the lower swivel to the base and pad it, pad the roller drum, and secure the end tight. Then put a sturdy garbage bag over the roller drum, and tape it tightly so highway winds will not bother it.
9) Put all mast wires inside the base of the mast and tape them in place to protect them from the mast being moved etc.
10) Remove masthead radio antenna and put any wires back into mast or tape them to the side of mast.
11) Using plastic wrap rolls, wrap the top of the mast, and the base of the mast, covering any sheet stoppers etc. Use duct tape to protect/lock in the wrap at the start and end of each layer, and at any stress points in the middle. The wrap and duct tape are easy to remove with a scissors and will provide some protection from road dirt etc.

Prep the boat (these steps are specific to my boat, but provide a framework):
0) Grease the MAX prop, check and replace any zinc's as needed
1) Put carpet scraps under each end of the boom and use heavy duty tie wraps (175lb break strength) to lock the boom so it can not slide in any direction. Can wrap the ends of the boom to protect the lines and tape before final tie down.
2) Pack lockers tightly so there can be no movement. In the anchor locker, I put 4 empty 5 gallon jerry jugs, the horse shoe life ring, a deflated inflatable bumper which locked these bulky items in a fixed place.
3) Remove front bow from Bimini arch and set it loose on the deck. Lower bimini down leaving the pivit point attached allowing the bimini to rest on cockpit hand holds. Tie the forward bow on top of the now lowered bimini poles and wrap it tightly and tie wrap it in multiple places. Pad where it touches the cockpit hand rails with carpet and lock it tightly to the hand rails.
4) Remove radar pole supports, lower radar mast and remove radar dome and base plate. Then pad the end and middle of the pole where it might rub. Easier to pad it now than when it is down and disconnceted.
5) Remove the radar pole pivot bolt, wrap the end in carpet and tie wrap it firmly in place to deck and to bimini arch.
6) Tape AIS antenna to the radar pole
7) Drop dingy to ground (put on carpeted blocks to keep engine off ground)
8) Remove davit poles and wrap together, wrap radar support poles and bimini poles into a bundle as well.
9) Wrap radar and bimini support poles with Vang and set on floor in cabin.
10) Lay shroud loops in floor in cabin padded with carpet, and tie them to the table support legs so they can not shift. Place the pole bundle next to them and tie together so the poles also can not shift. Place a couple of sails on top also tied to the table to make the whole stack solid. You can pack items like books in a bag in the corner of the floor under the table. It will be locked in by the shrouds.
11) Tie down genoa blocks and remove all blocks from mast step (Or wrap them all together and tape them if you want to leave them at mast base), stow in boxes under aft bunks
12) Stow dingy fuel tank in star aft locker with fuel filter (Mounted to shelf tank with Shrink wrap tape). Tie tank down and close off fuel vent.
13) Lock wheel and tape instrument covers on as well as tape all lifeline gates.
14) Look around below. My experience is things will try to shift aft, so the aft bunks are good spots for things. In my case, the radar dome, grill, boat hook, solar panels, spreaders (wrapped and taped together in pairs), genoa and main sails and all canvas are packed in the port aft bunk. I stow some boxes and the windex in the aft head, and in general, make sure there is nothing that can roll around in any lockers or cabinets. The fridge is a good place to pack things as well. Putting spare towels or drink holders in with glasses and plates help protect them and keeps things from shifting.
15) Do a final check of the deck, remove any dorade vents, and in general look at what could move in 70 MPH or more of wind. Make sure the anchor is locked down.
16) A good time to do any bottom painting or waxing as needed. Also a good time to do any other out of water work (rudder repairs, etc..)
17) Any dingy or outboard maintenance and flushing can be done at this time.
18) Double check all hatches are locked shut, all doors are closed and there is nothing loose down below or on deck.
19) Leave a key somewhere the truck driver can use to enter the boat if needed.
20) Double check your list of spares and locations of all stored gear/parts. Much easier to put things on the boat (like inflatable life jackets, or heavy items) and have them shipped with the boat, thant to remember them after the boat is out of town.

Time to load:
Not much to do at this stage but pay your yard bill, and let the trucker do their thing. The boat is moved to the truck, then blocked up, and then the mast is loaded and strapped down. Pretty soon, the boat is on it's way. In our case, the dingy can be placed on padded stands, or on the truck floor between the keel and the rudder. The Outboard is loaded on a simple stand mount located at the front of the trailor.

Putting it back together...
This tends to be a simpler and faster process if you have done any maintenace work before you shipped, but there is still a lot to get done, so I plan on 4 or 5 full days. It is important to clean and put anti sieze compound on the turnbuckles, and lanacoat the radio antena to ensure no moisture issues. Clean any corrosion or tarnishing on all parts before re-assembling them to make the polishing work a lot simpler.
When prepping mast, make sure to:
1) Pull wires back through exit hole in mast base and tape out of the way
2) Run all halyards, SSB antenna, lazy jacks, running backstay etc.
3) Pad spreader ends to avoid mainsail chafe down wind, grease the shroud end caps where they go into the spreader to make removal easier  when the mast comes down next. Be careful to use anti-corrosion paste on all SS bolts where they hit Aluminum.
The trick to put spreaders back on is to put long bolt through the bar and thread short bolt to the bar near spreader end. This way you can wiggle the spreader on and get the bar in the slot. Once it is in the slot, remove the long bolt until the spreade goes far enough in to aallow you to put the bolt through the hole int he main bar. This is specific to my Ben 46 spar, but without this trick, putting the spreaders back on is near impossible so I made a note here to job my memory.
4) In general, inpect rig, check all mast lights, and fix any issues while it is on the ground.
5) Clean, smooth and grease the mast step on deck as the mast is a tight fit, and any dirt etc can prevent the mast from sliding on cleanly when you step the mast.
6) put back on any pulpits etc that were removed for trucking
7) step mast, then connect wires from mast base into cabin (Radio, Wind, bow and anchor lights)
8) Put on boom, then vang, then blocks at base of mast, and run the lines back to cockpit
9) Put radar on radar pole and then raise pole
10) put back bimini arches
11) Tension rig and pin shrouds
11) Re-install masthead intruments, windex, and radio antenna
12) Put back on AIS antenna
13) Put main and main cover on
14) put up dodger (easier to put main on with dodger down)
15) put on Genoa
16) general clean up and wash boat.
17) Stow dingy on deck if needed