OK, let's get serious for a possible fix.
Open both Flip4Mac and Perian in your Syst Prefs and see if they actually open and work, and if so click any update options to see if there's an updated version.
If so, after any updated install, shut down (don't just restart) and reboot.
The next may be overkill but it sure won't hurt:
Download the Mac OS 10.6.4 COMBO Update from the Apple site.
- Shut down and bootup in Safe Boot Mode (hold down the shift key at the startup sound) and run the Disk Utility Repair permissions and verify disk.
- Open and run the COMBO updater and when completed repeat the above Safe Boot and repair stuff again.
Then after all that's done, reboot normally and then Go to your applications folder and open the utilities folder.
Open Java Preferences and click on the 2 Restore Defaults buttons.
If for some reason, your java preferences mysteriously disappears from your dock, reinstall Java for Mac OS X 10.6 Update 2 at Apple - Support - Downloads
but you shouldn't need to do so using the Combo and checking your Software Update just to make sure.
Then go back and open Java Preferences and restore defaults.
Shut down and boot up normally to your user account and hopefully your troubles will be over.
Doing so you have just done a major Mac OS maintenance routine that should keep you working properly until the next time...