After downloading the update, I can no longer watch videos online. Has this been disabled? How exactly do I reenable it?

At a recommendation from my school, downloaded and updated my computer against the recent Flashback software. Now, one night later, I am unable to watch online videos, as the plugins are no longer working. How do I reenable plugins? I cannot see any obvious way to do this via Java Preferences, and the box under Safari Preferences for "enable java plugins" is already checked. What has changed, and what can I do? Please be specific. Thank you!