Except space is cheap, and I need to flip back and forth between different projects. So it sounds like I will continue doing what I have been doing so that I do not have to keep flipping over to the Tomcat manager. It also allows me to keep datasource configurations, etc. separate.
MyEclipse should probably flip to the RAD/WTP model: Create a server project that contains configuration definitions, and associates with one or more Web Projects. That way I do not need to have multiple TomCat installs of the same version. Plus I can use Eclipse Team integration to check in (and share) server projects. It would need to contain major config data such as ports, datasources, etc.