In principle this is possible. Only catch is that if you specify a class in the 'java' package, the sun classloader will forbid it:
Exception in thread "main" java.lang.SecurityException: Prohibited package name: java.io
at java.lang.ClassLoader.preDefineClass(ClassLoader.java:480)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
at java.net.URLClassLoader.access$000(URLClassLoader.java:56)
at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
In order to circumvent the problem, you need to provide your extra classes on the boot classpath:
$ java -Xbootclasspath:/home/user/Desktop/:/home/user/Desktop/rt.jar java.io.Hack
hacked
You can then also override system files, for instance java.io.File:
$ java -Xbootclasspath:/home/user/Desktop/:/home/user/Desktop/rt.jar java.io.File
Error occurred during initialization of VM
java.lang.NoSuchFieldError: separatorChar
at java.lang.Runtime.loadLibrary0(Runtime.java:819)
at java.lang.System.loadLibrary(System.java:1030)
at java.lang.System.initializeSystemClass(System.java:1077)
(showing that we just overrode java.io.File)
So you can override system classes, the trick is that you must have access to the virtual machine. You can't do it on the fly, which of course is due to security restrictions.