locking skewers for the tires, gears, seat and handle bars.
an ugly color
At this point, they'll need an angle grinder to get anything valuable off the bike. It's more expensive but so long its not the standard of ever biker, bike thieves'll target easier bikes to steal off.
It's, once again, comes with infrastructure. When I moved to Germany from the country with no bike infrastructure, I only thought of a bike as an expensive stuff, but here I bought a used commuter for 40 Euro and it's fucking great. I love it, but if it gets stolen, I would be mildly frustrated and buy another one of those for 40 Euro the next day.
Think of it that way - whoever stole your bike was probably more happy to get it than you are sad to lose it. The total happiness in the world increased. So, whatever.