In my Xcode project's plist file, I can see the value for the key CFBundleIdentifier is:
com.mycompany.${PRODUCT_NAME:rfc1034identifier}
Obviously I will have to change com.mycompany to the domain name of my company, but I have no idea whether the rfc1034identifier should be removed so that it becomes:
com.mycompany.${PRODUCT_NAME}
Google did not help answering my question.
Does this rfc1034identifier affect the AppID that I should provide in the iPhone Developer program - Provisioning Portal?
The :rfc1034identifier just formats it (if needed) so there are no illegal characters* in the bundle name. You're unlikely to have a product that is called by an illegal character but it's not impossible.
I'd leave it in there but it's really up to you.
(Actually, most of the time I just hardcode the bundle - that way if the product name changes for any reason, it's still got the same bundle identifier when I come to update it in the app store)
*such as a space or a dot - they will be replaced with a dash so 'My Game' would become 'My-Game'