How can I export a QuickTime File with Chapter Markers from iMovie HD?
Looks like you can do it using Metadata Hootenanny.


  
    It allows you to edit and search the metadata that can be stored in  QuickTime movies (mov files), including chapters. Quicktime files support a large number of metadata options, but the QuickTime Player doesn't provide an easy way of accessing them. Metadata Hootenanny does.
  


You can read this forum thread for more info.