I am at present working on a solution (a transformation project) where the vendor packaged applications and their technologies more or less decide the deployment architecture, sizing and infrastructure requirements. There are cases where virtualization of servers can add up to 50% overhead on the server infrastructure. So the question is “do you decide on the deployment/hosting strategy first (where and how you want to deploy your application) before designing it or design the application and then decide the deployment strategy and infrastructure requirements ”.
With new paradigms in computing emerging day by day (ex. Cloud, grid and space based architecture, REST etc) application can now be designed based on how you plan to host them (i.e. what is the cost effective way of deploying them). However, you are bound to fixed application designs when you are using packaged applications (Most of the business application vendors like SAP, Oracle are still mostly in the standard client server or three tiered architecture space) and can not do much about it like my current project.
Normally infrastructure and operations are an afterthought with no consideration for them during application design. However, future trends are more towards using the existing/available infrastructure options and operations requirements to help drive the application design thereby closing the gaps between apps and ops in an organization.