Compilation of this code:
package javaapplication1;

public class Main {

    public static void main(String[] args) {
        @SuppressWarnings("deprecation")
        java.rmi.RMISecurityException ex;
    }

}

with "-Xlint:deprecation" produces:

/tmp/JavaApplication1/src/javaapplication1/Main.java:7: warning: [deprecation] java.rmi.RMISecurityException in java.rmi has been deprecated

This does not seem right, as JLS 9.6.1.5 says that:
"a Java compiler must not report any warning identified by one of S1, ... , S k if that warning would have been generated as a result of the annotated declaration or any of its parts"

Tested this on:
[snip]/jdk17/bin$ ./java -version
java version "1.7.0-ea"
Java(TM) SE Runtime Environment (build 1.7.0-ea-b18)
Java HotSpot(TM) Server VM (build 1.7.0-ea-b18, mixed mode)
Another case where the @SuppressWarnings("deprecation") does not work correctly:
package javaapplication5;

@Deprecated
public class A {
}

package javaapplication5;

@SuppressWarnings("deprecation")
public class B extends A { //reports "A is deprecated" here

}