The system classpath is available to all code running on the server. If you put something in an ejb's Manifest Class-Path, then that jar is accessible only to that ejb. Actually, the way WebLogic's ClassLoaders are set up, that jar will be accessible to all ejbs and webapps in the application. If you put a jar in WEB-INF/lib or in the webapp's manifest, it is only accessible to servlets, jsps, tags, etc in that webapp. I don't think the EAR's manifest is considered (at least the spec doesn't require it and WebLogic doesn't look at it).
subject: difference between Classpath setting in Manifest file and AppServer classpath