stratosg

Writing a post with footnotes has never been easier and cleaner before. All you need to do is anchor a footnote at any point and then write it on the end of the paragraph or wherever it fits you.
Usage
To anchor a footnote use the {{FOOTNOTE_NUMBER}}. Then to write the body of it you need to embrace it with [[FOOTNOTE_NUMBER]]. Here is an example:
—— document starts here ——- 
Lorem ipsum dolor sit amet, con sectetuer adipiscing elit, sed diam 
tempor incidunt ut labore et dolore magna ali quarn erat volupat.{{1}} 
venian, quis nostrud exerci tation ullamcorper{{2}} suscipit laboris 
commodo consequat. Duis autem vel eum irure dolore
[[1]]This is the first footnote.[[1]] 
[[2]]This is the second footnote.[[2]]
This is the next paragraph. Lorem ipsum dolor sit amet, con sectetuer 
adipiscing elit, sed diam nonnumy nibh euismod tempor incidunt ut 
labore et dolore magna ali quarn erat volupat. Ut wisi enim ad minim. 
—— document ends here ———
When the document is parsed, the footnotes that are between paragraphs will be removed from where they are and placed at the end of the document. The {{1}} will be replaced with an anchor link to the footnote. The footnotes will be a list having and anchor link back to the place the text has it. Here is what roughly the above text will look like after parsing:
—— document starts here ——- 
Lorem ipsum dolor sit amet, con sectetuer adipiscing elit, sed diam 
tempor incidunt ut labore et dolore magna ali quarn erat volupat.[1] 
venian, quis nostrud exerci tation ullamcorper[2] suscipit laboris 
commodo consequat. Duis autem vel eum irure dolore
This is the next paragraph. Lorem ipsum dolor sit amet, con sectetuer 
adipiscing elit, sed diam nonnumy nibh euismod tempor incidunt ut 
labore et dolore magna ali quarn erat volupat. Ut wisi enim ad minim.
FOOTNOTES 
1. This is the first footnote. 
2. This is the second footnote. 
—— document ends here ———
The up arrows and the [1] and [2] are the links. There are a few options that you can tweak, for now it’s in the code. Please refer to the plugin’s homepage at: http://www.stratos.me/wp-plugins/yafootnotes
<h3>Requirements</h3>
None what so ever…
<h3>Credits</h3>
Mr. Mike Nichols from http://anxietypanichealth.com/ inspired me, motivated me and helped me debug.
<h3>Contact</h3>
Suggestion, fixes, rants, congratulations, gifts etc to stratosg@stratosector.net 
Also visit the plugin’s page at http://www.stratos.me/wp-plugins/yafootnotes/

YAFootnotes

Yet Another Footnotes (YAFootnotes) is a plugin that gives you the ability to add footnotes to any text you are writing.

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.

YAFootnotes vs jQuery Hover Footnotes