Actually Apple does have a decent document on setting up iPhone in the Enterprise.
Apple - iPhone in Business - Integration
That being said I work in a vertical with many security / regulatory demands and earlier this year we removed support for iPhone. This past summer we also removed support for all over mobile devices but Blackberry. Many reasons came into this decision but the simple fact is device management and security on other platforms compared to BES is woefully lacking.
We hear daily from the iPhone users and trust me they are a vocal group. So I have an ongoing list of the reasons why we do not support iPhone. It's really a decision your org needs to make about mobile security, management. This is by no means a perfect decision and for those orgs with less regulatory concerns not as big an issue.
This isnt just an iPhone issue really, there is a growing number of devices that to me are just consumer focused. Blackberry is enterprise focused and provides granual control if you so desire. I doubt Apple will ever allow that level of control as they want that iTunes / AppStore revenue stream.
This is similar to my other favorite topic - Personal liable mobile devices vs. Corporate liable. We are strictly CL only, period. People don't like it but this was decided by multiple people making much more then my pay grade, no company data is to be synced to a PL device. It doesn't save us money and is just a risk. Not to mention the gray area about who supports what and where that line is so I'm happy to have that policy as again it is asked OFTEN.
Anyways sorry to ramble. I've attached my iPhone issue list if it helpful to anyone.