Oh yea, the reason you can’t deploy it as a dependency of the Web project is because it’s an EJB project.
It sounds to me you just have to restructure your deployment model. If you have an app that has EJBs and Web modules, what you need to do is create an Enterprise Application Project, and mark *those* projects as modules of the EAR project.
Then you need to mark any common library projects as references of the EAR project as well, and remove them as dependencies of the web project. WHen you deploy the whole thing MyEclipse will package it all up nice and pretty and deploy it as an EAR for you. More information here:
http://www.myeclipseide.com/documentation/quickstarts/earprojects/