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The usual way for downloading youtube's flv files used to be to double-click on the conspicuously largest file in Safari's activity window (cmd-option-a).
For some reason doing so now triggers viewing the video using a plugin. The possible culprits are perian and vlc. Disabling perian doesn't help, and vlc does not seem to include a plugin. What to do?
Hold Option while you double click on the file to force it to download instead of play. If you have something downloading already (or are using an older version of Safari), you can also copy from the activity window and paste into the downloads window.
