I am new creating apps for iPhones but I interested in developing few
but need some direction.

Our organization has a website that has public and protected content
for authenticated users.

The thing is that our system is using the Integrated Windows
Authentication system on an IIS...which pops the new windows for
credential (not form authentication).
I don't know how the iPhone will response to the popup windows
authentication system.

Does anyone know how I can deal with this situation? Any work arounds?
I think asp.net offers
Form Authentication against Active Directories or LDAP but not sure.

Any ideas would be greatly appreciated.

Thanks.

ozz

Have you simply just tried it?

"I think asp.net offers
Form Authentication against Active Directories or LDAP but not sure"

This is indeed possible using a custom membership provider in your
application