This has now been upgraded and superseded. Check out the latest version.
You can now choose whether or not the numbered links in the text should display as superscript or not.1 You can now also customise the backlink text. Many sites like to use this little guy: ↩ (↩).2
You can access all the options in the Footnotes tab of the Options section in Admin.
I have kept comments closed on this post.
Please use the original post to make comments on the Footnotes plugin Feedback here and bugs and feature requests here. You can also view all the changes there as well. Here is the download link if you just want to get straight to it.