Follow these precautions to make sure your motorcycle is transported properly and with transporters that are qualified.

[edit] Steps

Good safety precaution: drain your gas tank and remove your battery. You can also opt to crate your motorcycle at this point.
Wash your motorcycle even if it will be shipping on an open trailer. You want to be able to spot any chips, dings, or nicks before shipment.
If you are not removing the battery and your motorcycle has an alarm, disarm it before shipping.
Be sure to secure any loose parts and specialty items such as exhaust, saddle bags, tank bags, hard luggage, fairings and anything else that could get in the way during transport.
Make sure that your tires are properly inflated and that you don't have any fluid leaks.
Have a specific list with any problems your motorcycle may have. Your carrier will want to know of such things during the loading and unloading of your motorcycle.
To prevent disputes of possible damage during shipment, make a report of any existing damage prior to pickup. You may also want to take dated pictures of your motorcycle.
Also make sure to fold in any parts that can be folded such as the side mirrors. And lock the handle bar if possible.
Be sure to avoid shipping brokerage sites who don't verify DOT Licence credentials (i.e. uship.com ...) - these sites often allow unlicensed shippers and can result in your property being stolen.

[edit] Tips

Locate a reliable motorcycle transporter. See the links below for some transporter options.

Do not ship with cycle in gear. Leave the bike in neutral. Engaged transmissions during shipping can cause internal damage.
Do not ship motorcycle with title and key, and always get a bill of lading receipt with the shippers information and condition of bike listed