Index: java/org/apache/catalina/loader/WebappClassLoader.java
===================================================================
--- java/org/apache/catalina/loader/WebappClassLoader.java	(revision 1003433)
+++ java/org/apache/catalina/loader/WebappClassLoader.java	(working copy)
@@ -2179,6 +2179,9 @@
     @SuppressWarnings("deprecation") // thread.stop()
     private void clearReferencesThreads() {
         Thread[] threads = getThreads();
+
+        // Is checking for a null value better than using the synchronized method?
+        boolean shuttingDown = System.getProperties().containsKey("org.apache.catalina.shuttingDown");
         
         // Iterate over the set of threads
         for (Thread thread : threads) {
@@ -2194,6 +2197,11 @@
                     if (!thread.isAlive()) {
                         continue;
                     }
+                    
+                    // Skip daemon threads if Tomcat is shutting down
+                    if (shuttingDown && thread.isDaemon()) {
+                        continue;
+                    }
 
                     // Don't warn about JVM controlled threads
                     ThreadGroup tg = thread.getThreadGroup();
Index: java/org/apache/catalina/startup/Catalina.java
===================================================================
--- java/org/apache/catalina/startup/Catalina.java	(revision 1003433)
+++ java/org/apache/catalina/startup/Catalina.java	(working copy)
@@ -633,6 +633,8 @@
      * Stop an existing server instance.
      */
     public void stop() {
+        
+        System.setProperty("org.apache.catalina.shuttingDown", String.valueOf(System.currentTimeMillis()));
 
         try {
             // Remove the ShutdownHook first so that server.stop()