I previously discussed Tomcat discovery in the OM2012 RC version in this post. If you run Tomcat as a service on Windows you still have to manually discover it.
There has been a minor change since OM2012 RC, BeanSpy and the Powershell scripts isn’t included with the files in the JEE MP anymore.
When you import the MP’s, BeanSpy will be placed in the Operations Manager folder. Look in your Operations Manager installpath, i.e. “C:\Program Files\System Center 2012\Operations Manager\Server\Health Service State\Resources\”. Search for BeanSpy to locate them. Under the same path you can also locate the Powershell scripts needed to manage Applications servers. Search for *.ps1 to locate them.