As nicely stated by the Javadoc for org.apache.commons.discovery.tools.ManagedProperties, "System properties are global in nature, so using them easily violates sound architectural and design principles for maintaining separation between components and runtime environments." Lucene's use of system properties makes it so that one web application that uses Lucene can break another web application that uses Lucene.
Both org.apache.lucene.index.SegmentReader and org.apache.lucene.store.FSDirectory use system properties to locate an implementation class. Because of this, two applications can step on each others' toes.
So, I have two webapps running in Tomcat. One uses the Compass Framework which sets the SegmentReader implementation class to org.apache.lucene.index.CompassSegmentReader. My other webapp tries to initialize SegmentReader in a different classloader, and it fails with an ExceptionInInitializerError because it can't load that class. If I get lucky, the non-Compass webapp loads first and things run smoothly.