Like dressing for the cold this is best done in layers. Here they are in progressive layers: FACTORY LOCKS, DISK BRAKE LOCKS, LOCK AND CHAIN, ALARMS AND HOME SECURITY.

Factory locks
The built in fork lock and ignition switch on your motorcycle take a pro a couple of seconds to get around and a beginner a minute or so. However they are better than nothing. If your bike is going to be out of your sight lock your front fork! It only takes a second and it may keep a thief from just rolling your bike away.

Disk Brake Locks Lock and chain

Cables A personal favorite of mine. When I travel I carry a couple in my saddlebag. They are lighter than a chain. With two cables I have a lot better chance of reaching a solid object. They are often hard to cut with a bolt cutter.

Factory AlarmsAfter market Alarms
Aftermarket alarms are as good as or better than a factory alarm depending on what you buy. Even the cheapest alarm is much better than none. When you install one make sure you do it right. Use the correct gauge wire and the best quality connectors you can get. Motorcycle wiring is subjected to heat and vibration and susceptible to shorts and bad connections. Do it right!

Immobilizers.
and remote starters I do not recommend these. The added complexities of these systems make them more prone to failure. The KISS principle applies with alarms. Keep It Simple Stupid ! There are too many opportunities for one of these to fail and strand you far from home. Having said that a very nice option is a simple toggle switch installed out if sight that shuts off the power to your coil. As I mentioned before a good wiring job is essential. Do it right, use the correct materials and remember to use a switch that is rated for outdoor always to remember to flick the switch otherwise you will run down your battery!

General home security
A few precautions that make your home more secure also help protect your bike. Motion sensitive lights If your bike sleeps outside at night install a motion sensitive light nearby.

Fences and gates
Fences are always a good idea. If you have a gate lock it.

Dogs
Always a good idea if you are a animal lover. Try to store your bike where old Rover can keep an eye on it.

Keep your bike out of sight.Burglar Alarms
If possible store your bike in your garage protected by a monitored alarm system.. If your home does not have a burglar alarm. I recommend an inexpensive battery powered one mounted in your garage next to the bike. They cost about 29 bucks.

Getting your bike back
Marking
Mark the various components of your bike. A simple scribe or similar device can be used to put your identifying information on the back or bottom of various components without defacing your bike. I typically use my drivers licence number. Note: I put clear fingernail polish over my information to prevent rust.

Have your info handy
Write down your VIN and Licence plate numbers and keep them in your wallet. If the unthinkable happens and your bike is stolen when you are on the road the police will need this info to find your bike. A photo will also help if you have customized your bike. Police love to get their hands on thieves make it as easy for them as possible.

Space age and cruel methods
If you have the money a satellite tracker such as LoJack can help find your bike.

A customer claims that he uses an electric fence charger to protect his trail bike. A $30 electric fence charger will give someone a big surprise! Remember to park the bike on a rubber mat or some other insulator to keep it from being grounded. NOTE: This may be illegal, dangerous and it may fry expensive electronics. After being knocked on their butt the thieves will just disconnect them. If you do this it's at your own risk! This is included for amusement purposes only!
I have had one bike stolen and never seen again, it sucks. I hope this simple guide helps you avoid the same experience.