In a recent article in Computerworld there was a discussion of the phenomenon of cloud computing expanding uncontrollably in an enterprise. Cloud was compared to the client/server and departmental computing shift that took place in the late 80s and 90s. I agree that this is a concern, but as presented the argument was focused too much on an internal IT orientation. An organization's shift to Cloud computing is not about hardware -- that is now someone else's concern. I've tried to stop using the term cloud computing, since many people shift to thinking about hardware at that point and instead talk about cloud techniques or cloud architectures.
A primary issue with cloud a need to understand how business value is generated (when, where...) for the enterprise and how to get the information in and out of the organization securely and reliably, without giving up the flexibility to move to another service provider at a later date. Some people think about getting their data into a service provider but not about what to do when requirements and capabilities shift or another commodity service provider offers a better approach at a later date. As you move up to higher levels of cloud technologies these issues can be much harder to overcome.
Being business goal oriented is of primary importance -- if you're not focused on the corporate goals it doesn't matter how many new compute cycles can be brought on line. There are numerous issues that CIOs and IT personnel are familiar with like: service (data and process) integration, security and enterprise data management... These are part of any viable Enterprise Architecture and the IT organization can help the business by providing structure and insight. These issues in the EA space have been defined via standards efforts like TOGAF from The Open Group and the issues classified by techniques like the Zachman framework.
Just because an organizations shifts to a cloud service, it does not mean that all these concepts will be thrown out. Client/server and Web techniques didn't make everything known about computer and business operations before their introduction irrelevant, cloud is an evolutional change from the business perspective. Cloud is part of a next wave of computing but only a part.