iMore has a really great look at the 16:9 iPhone, how it might show up, how it’ll be used, the justification for it, etc.
With all that in mind, the least likely option — though the easiest for developers — is for Apple to keep the app space the same on a 16:9 iPhone as it is on the current iPhone, and use the extra pixels exclusively for new and updated iOS features.
Really good article, worth the read. Full or rumores and speculation of course. :)