For my commuter I use zip ties and/or glue to secure things to the bike and common sense as to where I park/lock my bike. I generally keep my tool bag in my courier bag, so the only thing that stays on my bike are lights and a cheap computer.

It will take a motivate thief to get my lights and it won't be something he can do in less than a minute. I haven't had anything stolen off my bike in at least five years, three of which I locked my bike up outside.