http://captiontube.appspot.com/

=]

From their help:
<<CaptionTube is a utility for adding closed captions to YouTube videos. After you import a video, you play the video and add captions as needed. When you are done, you export the captions and then upload to YouTube.>>

Hmm, their content negotiation seems to be broken. I'm getting secondary languages like German or Japanese instead of my preferred language, English...