There is an interesting group of articles on bike theft, alarms/immobilisers and trackers in this month's (well, April's) edition of Ride magazine. I'm generally a fan of alarms and I've chased off a yoof who triggered the alarm when trying to wheel the Kawasaki away, but I agree that you should use a good lock and chain as well.
The 12-year-old Datatool on my ZX6 is still working well, as is the Meta on my R1. As the article says, the alarm is always the primary suspect when anything goes wrong but it's often not to blame.
The Ride article includes an example where a stolen KTM was found "abandoned" behind a block of flats and it was assumed that the thieves "couldn't start it or find any other use for it." In fact what happens is thieves leave a vehicle for a few days in case it has a tracker. If it's still where they left it they know it's safe to take it home.