This section is incomplete, and will eventually show the specifics (and hopefully examples) of configuring and using ModeShape in non-AS7 servlet containers and application servers. If you use a particular pattern or wish to contribute an example, please let us know!
For the most part, the best way to use ModeShape within a web application deployed to Tomcat, Glassfish or other containers or application servers is to simply embed it into your web application. At that point, it should be very similar to ModeShape in Java applications.
If you have several web apps that share the same ModeShape repositories, embedding ModeShape into each and using the same configuration files should work (as long as the apps share the same classloader). Or, you could create a single web app to manage the ModeShape repositories (including registering them into JNDI, either via configuration or via programmatic use of JNDI) and have the other web applications simply look up the repository as found on Using Repositories with JCR API in EAP.