This site describes how to copy YouTube annotations across videos. It essentially helps you liberate your annotations data and modify it at will.

This page was created by Stefan Sundin. Read blog post. Last modified 2012-02-12.

1. Use Firefox! The XML code will only run in Firefox!
2. Fetch annotations from an existing video:
    
3. (Optional) This is your chance to do things the YouTube developers did not think of.
   A few examples:
   If you want the annotations to last the whole video, you can edit the end time to something like t="1:00:00.0".
   You can change the width and height of the annotations to sizes that the normal editor will not allow.
   You can remove the ugly padding that YouTube added to notes around 2012-01-14. Simply remove the <padding/> tags.
   While you can change link urls to external urls, they will not work. The video will have to be marked by Google to allow external urls (iv_allow_external_links=1 in flashvars).
   You can make a video automatically repeat by inserting a pause annotation at the very end of the video with 0.1s in length (example). You can do this in the normal annotation editor.
   Let me know if you find a nice trick!
4. Paste the XML into the box below.
5. Insert your username in the text field below. Make sure you are logged in to this user on YouTube.
6. Fetch video_id:auth_token pairs to the videos you want to copy the annotations to.
   You can use this Greasemonkey script to help you do that.
   A text field with the video_id:auth_token pair will appear in the lower right corner of the "edit annotations" page.
   A download link for the annotations will also appear.
   Flashblock is also a good idea.
7. Open the Error Console (Ctrl+Shift+J).
   Click the Update button. This will submit the XML.
   If nothing happened, you will see an error message in the Error Console.
   The annotations have now been saved as a draft.
8. Click the Publish button if you also want to publish the annotations.
9. ???
10.Profit!

To delete annotations, you can use this syntax:
<document><deletedItems>
<deletedItem author="X" id="annotation_Y1" />
<deletedItem author="X" id="annotation_Y2" />
</deletedItems></document>