Since 2.4 it is possible to get a war file of a Mendix application. You can deploy this file on a Java EE compatible application server. However, due to the difference among application servers in classloading it doesn't work on all servers that well.
In 2.5 we have fixed these issues and added comprehensive support for Java EE compatible application servers. We have built a M2EE server which can be deployed on application servers. After that you can connect to this M2EE server using HTTP/JSON to upload models, start and stop one or more Mendix Runtimes, etc.