A clever solution used by e.g. Shopkick is to play a very high-pitched sound of a certain frequency on the store sound system and pick that up with the device microphone.

I don't know if Apple is using this here. I bet they're instead identifying it by store Wi-Fi, since Apple stores all have that already. But for stores without Wi-Fi, the sound system trick works well since all stores have sound systems already.

I doubt that either the store sound systems or the phone's microphones perform well at frequencies above the audible, though, so it may not be quite the drop-in solution that it appears to be at first.

There are a bunch of different solutions to this problem being explored. Being able to give provide location context-specific services in your applications is something that I personally think is going to be a huge thing in the next few years.

My current company is actually providing developers with a service (currently Android only) to provide better location contexts in their apps.

If you're interested you can take a look at our homepage from my profile. We just launched our public beta this week so if this sort of thing interests you as an app developer, please check it out :)

I would assume over time that geo-location coordinates will get more accurate and that there will be an assumption of which place you frequent the most will be given priority over other apps.