The cloud is certainly going to change some things about malware infection. When a desktop is reset to clean state every time an employee logs in, you now have to wonder how malicious attackers are going to maintain persistent access to the Enterprise. This is similar to what happens when an infected computer is re-imaged only to end-up infected all over again.
There are several ways to maintain persistent access without having an executable-in-waiting on the filesystem. Memory-only based injection is an old concept. It has the advantage of defeating disk-based security. One common observation is that such malware doesn't survive reboot. That is true in the sense that the malware is not a service or a driver - but this doesn't mean the malware will go away. Stated differently, the malware can still be persistent even without a registry key to survive reboot. This applies to the problem of re-infection after re-imaging (a serious and expensive problem today in the Enterprise) and it also applies to the future of cloud computing (where desktop reset is considered a way to combat malware persistence).
The most common method for persistence without reboot is re-infecting the system from a neighboring, already infected system. It has sometimes been called the "Hack Finn" model - two or more malware programs that know about each other. Unless you kill both of them simultaneously the one will re-create the other. In today's world, the neighbor doesn't need to be physically nearby - it can be anything that has some access path to the other machine. This neighbor could be a social networking peer, a shared desktop (think exploited .ini), or a machine with lateral domain credentials.
Another way to maintain access is to store crafted (exploit) data in a commonly used document - think PDF exploit but for google docs. User's in a cloud based environment are going to have persistent data storage, whether this is up in the cloud or down on a USB stick. When the execution environment is constantly reset, as it might in a desktop cloud, the attacker can move method of persistence to the data itself. The malicious code must obtain execution cycles - think of the cloud based desktop simply as an execution space. The user opens said boobytrapped document every day as part of their work, and the malicious code activates. Or it can be delivered via a system used on a daily basis, such as an exploited image on an ad-banner, or the little calendar program in the corner of your timecard system.
For the window of time the user is interacting with the desktop, the code has execution cycles. This is when data is most at risk - this is when other documents are open, other social network contacts are online, and the user's access token is live and can be used to access other resources.
Remember, the attackers always adapt to new environments. The cloud just provides new ways for our adversaries to attack us.