I would say that if the application is critical to the department, and you can support the application in the current enviroment you should deploy it now to a physical server. When you get VMWare you will I assume be getting the Virtual Center as well. This will allow you to get the VM Converter product which makes converting physical machines to Virtual Machines a piece of cake.
If you need to move the machines with less downtime look at a product called Platespin. This is an excellent P2V tool which requires about 5-10 minutes of downtime per server that you P2V.
Agreed, consider deploying critical application now on your physical servers. Then you can just use tools to convert physical environment to a virtual environment via VMWare convertor and move configuration settings via Scriptlogic’s Desktop Authority or something. The general rule for today I thinks is to move forward and don’t simply sit and wait. Waiting usually doesn’t give a profit.