Captioning in Quicktime with Media Mill
The Media Mill beta site has a new feature, which allows you to caption Quicktime (and video for ipod/iphone) files, in addition to the existing flash capability.
All you need to do is add your captions to the transcript field (in the same DFXP format as always) and then create a quicktime derivative. The captions will be baked into the file, as a true captioning track. Then you can choose to turn it on and off during playback. In Quicktime Player, it's under the view menu, in iTunes it's under Controls->Audio Options, and on the iPhone it's in the iPod settings menu.
When you're watching it in the browser, just right click (or control click on a mac) on the video and choose "show captions." Here's an example.