Cloud and Windows are not really in love at the moment. Because paying a license $150 per VPS is maybe too much. And there is no Cloud Orchestration system running on windows. It doesn't mean you cannot find a VPS with Windows, but for a VPS with 6GB RAM the price is $25 more per month to run Windows server 2012.
The major a currently OpenStack, OpenNebula & VMware vCloud and they are all build on linux.
Windows is a viable choice if your marketing to customers that need specific Microsoft functionality that linux does not provide. Their is still a big market looking for windows hosting.
From your post I assume your asking what OS is best to use on your cloud based VPS, CloudLinux is best.
If your looking to create a cloud, Linux is the only choice imo. @virtubox covered the best virtualization software, OnAPP is great if your looking for a big enterprise grade cloud but it also has a price tag to match. .
CloudLinux functions the same regardless if it's on a dedicated server or container based VPS. The 'Server' still views the operating system the same way.
If your using a dedicated or a VPS you will still have the features of CloudLinux.
It should be called ContainerLinux but I suppose they used the cloud buzzword to help marketing and sales.
Both Windows and Linux OS are used for Cloud VPS. Both have their own pros and cons which you will need to study. After understanding what features are best for you from both, you can decide which OS will be the best for your Cloud VPS.