There is no (legal) way to distribute apps to a regular iphone except through the app store.

If you jailbreak it, then there are other options, but that would be eliminating 90% of your market... and plus, Apple might come after you since it would be a violation of your developer agreement with them.

I think the "in house distribution" refers to specialized apps used exclusively in a closed network, say an app that runs only on, say all iphones that IBM staffers have or something. It is definitely not an alternate distribution method, otherwise no one would use the app store.