It seems Apple has added an option to the QuickTime Preferences in the System Preferences, and have opted to set the default action to disabled.

Since Flash is quite pervasive on the web, it isn't beyond reasonable doubt that Flash could be an attack vector for malware on OS X, the way it has on Windows, so I guess I could see the logic in having it disabled by default. Seems unlikely that QuickTime would be at fault, when most people use Adobe's Flash plugin for the majority of their content.

However, as Martin Karr noticed, this breaks Apple's own applications, such as iCal's alarm clock graphic in notification windows.

Set it back to enable QuickTime to take care of your Flash content when applicable. Although it won't have the latest features of each new release, the QuickTime team doesn't usually let Flash support fall behind a version number or so. I certainly trust it more than Adobe's plugin.