An upgrade of Mac OS X broke your deployed applications.
You thought Apple knew what it is doing and accepted a Software Update. Hopefully you did this on a testing server before you did it on something that people depend on. And hopefully you had made a copy of your httpd.conf file before you did anything, or have a backup of that file available. There are a few things that may have happened. First, it may have nothing whatsoever to do with WebObjects. Do a google search for news about the update and see if there are fixes to any issues. For example, doing an upgrade around 10.6.4 or 10.6.5 would break /usr/bin/apachectl, which is a script, but the fix was pretty trivial.
If these steps fail, check in with the mailing list. Explain what you have done and what you are seeing. And explain that the wiki was incredibly useful and more stuff should be documented!
ERXExtensions have not been initialized.
When your application starts running you might get the message:
ERXExtensions have not been initialized. Please report the classpath and the rest of the bundles to the Wonder mailing list: Remaining \[WONDER:JavaXML, JavaFoundation, ERJars, JavaEOControl, JavaWOExtensions, JavaEOAccess, JavaJDBCAdaptor, JavaWOSMIL, ERExtensions, JavaWebObjects\]
Check your main routine - it should be: