I just read this interesting article: http://www.itworldcanada.com/news/absolutes-iphone-manager-helps-it-avoid-itunes/141990
It talks about this product called Mobile Device Manager, created by a company called Absolute. Looks like it can replace iTunes in large businesses, so that the IT departments of said businesses can roll out iPhones and then create apps for them without having to go through the iTunes Store. It allows a bunch of data-gathering and lockdown for said IT departments, as well.
Very expensive product...
http://www.absolute.com/en/products/absolute-manage/absolute-manage-mdm.aspx
Integrates with their gernal deployment tool or Microsoft Config manager.
Enterprise app deployment (IE in house apps) is already supported through less centralized methods
http://developer.apple.com/library/ios/#featuredarticles/FA_Wireless_Enterprise_App_Distribution/Introduction/Introduction.html