Scott,
I've moved the VOD and the SOSample into their own ears and everything seems to be working just fine now with the trick of having the initial default context in the red5-context.jar has you've mentioned. It's now available for download through my blog.
I'll try to look into the logging issue since that is in-fact very annoying. I'm running JBoss through Eclipse and that kinda helps to manage it. Still, for production environments one needs to be able to disable it or redirect it somewhere else. I believe that we might be able to configure JBoss logging to filter and prevent from logging everything "org.red5.*" and "o.r.s.*" to the stdout.