Ok, I'm not the first person to have this problem... skip to bottom for my solution. I'm just getting this out there... it might be my unique problem of everyone on the Internet.
Some people reported that plugin support just got turned off... and using Preferences to re-enable it fixed it. My problem however turned out to be much more complex.
I finally stumbled across the fact that Help -> Installed Plugins on my MBP was entirely blank... not a single plugin was working... so I moved them all... and then just put Flash back... it worked. So then I started putting all my other plugins back and restarting Safari each time. When I copied JavaPluginCocoa.bundle back the plugins page went blank again.
Since I had just installed a Java update earlier I downloaded that same update from apple.com and re-installed.
Problem fixed. Ugly test flash graphic you've never looked so good.
Update: I just found out my sound (YouTube, etc) still didn't think. This fixed it.