I use a combination lock bike chain (the thin cycle lock kind that are easy enough to bolt cut). Additionally, I always cover my bike with a rain cover, even in summer weather, and that seems to have made a major difference somehow.
Finally, and most notably, I installed an alarm under the fairing, close to the engine. This alarm goes off if the bike is nudged. They are cheap, quite sensitive, and awfully loud. Plus, just the act of pointing your keyring at your covered bike, and the bike responding with a very loud beeping, is enough to deter most bystanders.
As long as I remain within earshot of the bike, which is easy to do all of the time for me, it's generally pretty resistant to theft.
I live in a house with no garden and the bike is parked overnight on the pavement outside my house. Over the last year there have been 2 occasions where I leaned out of the window, after hearing the bike give a warning beep, and saw youths walking quickly away from the bike.
No solution is foolproof, but the alarm really has given me a lot more security, and seems an extremely effective way to deter theft. You can get one for <20 from amazon. The batteries only last a few months, but are easy to replace, and as long as the alarm is fitted somewhere that's not too easy to smash with a hammer, there's no way a thief is going to remove your lock without you knowing about it immediately.