Okay so I just moved my most stable app into the organisation.

In case it helps anyone here's what I did:

1) Go to the repository in your normal GitHub user and click Admin.
2) Rename the repository to a more suitable name if necessary (all my repositories have the prefix harmattan to distinguish them from other platforms, this is redundant in the organisation). Ignore the redirect warning.
3) Wait for the rename to be complete, then in Admin go to the red "Danger Zone" at the bottom and Transfer the repository to "harmattan" (I had to type it manually no helpful list of owners came up).

If you want a convenience redirect, or to not have to work directly within the organisation:
4) Go to the harmattan homepage and wait for your repository to appear. Click on it and fork it back to your personal profile.
5) Go to the forked repository click Admin again (make sure it's your personal one) and Rename it back to what it was before. I think Git clients will still be happy but your fork will have lost some of the GitHub extensions like issues and downloads. You can manually re-add these if you had download links (such as on a blog) by grabbing them from the harmattan version of the repository.
6) Remember to push/pull back to the organisation every so often if you are releasing new versions into your personal repository.