Lance Willett

JQuery Hover Footnotes lets you add footnotes with qualifiers of you’re choosing, then dynamically displays them on hover-over. So you can easily add footnotes to a post by wrapping them in qualifiers, then they will dynamically display in a jQuery hover popup when the user mouses-over the footnote link. There is also a settings page where you can change options like the footnote formatting.
Features
-Numbers, Words, or ANSI characters can be used as footnote reference marks 
-Footnotes can be superscript, subscript, or normal text 
-Footnotes can be placed in page footer or hidden 
-Popup/Hover footnote can be turned on and off.
Usage
To anchor the footnote reference mark/number, use {{FOOTNOTE_NUMBER}}. Then just embrace the actual footnote text with double brackets [[FOOTNOTE_NUMBER]] Footnote text [[FOOTNOTE_NUMBER]]. The footnote text can be placed either inline or at the bottom of the post, the plugin will find them and auto place them in the footer area.
So this is what you would write in the post window…
This is my post and I want to add a footnote{{1}} in the text. By default it will appear as a superscript.
[[1]] My Footnote. [[1]]
see the plugin webpage or the screenshots for examples.
visit the sites page <a href='http://restoredisrael.org/blog/961/footnote-plugin-test-page/' rel="nofollow ugc">here</a>
<h3>Credits</h3>
This plugin is a fork and combination of several other plugins.
PHP- 
stratos at <a href='http://www.stratos.me/wp-plugins/yafootnotes/' rel="nofollow ugc">YaFootnotes</a> and <a href='http://anxietypanichealth.com/' rel="nofollow ugc">Mike Nichols</a>
<h3>Contact</h3>
Developed by Lance Weaver. 
To contact, leave a comment on the plugin <a href='http://restoredisrael.org/blog/961/footnote-plugin-test-page/' rel="nofollow ugc">website</a>

jQuery Hover Footnotes

JQuery Hover Footnotes lets you add footnotes with qualifiers of you're choosing, then dynamically displays them on hover-over.

Andrew Nacin

Create simple, elegant footnotes on your site. Use the <code>[ref]</code> shortcode and the plugin takes care of the rest.
Example usage: <code>Lorem ipsum. [ref]My note.[/ref]</code>
If you paginate your posts, you can optionally move your footnotes below your page links. Look under Settings > Reading. Footnotes will still appear as normal for posts that are unpaginated.

Simple Footnotes

Create simple, elegant footnotes on your site. Use the [ref] shortcode and the plugin takes care of the rest.

jQuery Hover Footnotes vs Simple Footnotes