There are simple APIs on iOS (and I believe on Android) which allow you to protect private keys and other data in local storage. Once the iPhone 5S with biometrics comes out (90% likely in September), this will be even more meaningful.
And yes, the pals at AuthenTec had some cool biometric and related stuff when I worked with them :), before they were swallowed by Apple. I'm certainly looking forward to what Apple will launch ... but a fingerprint does not magically solve all the issues.
HSMs can do this (no one really does, though); smartcards can too. The problem is no one wants to physically plug a smartcard into a phone, so you're stuck using stuff physically built into the phone. The alternative would be a bt 4.0 le cardholder which talks to the phone, and contains either an internal smartcard or a smartcard slot.
For DOD, there's a badgeholder for the CAC which speaks bluetooth (old, 2.1 I think) to the RIM Blackberry. Updating that to 2013 to work on the iPhone would be pretty awesome, using 4.0le, particularly with a decent smartcard (not sure what the state of the art is; I remember screwing with old javacard stuff with the iButton which sucked.)
SIM cards come to mind.