Yoinked from the og readability:

   /**
     * For easier reading, convert this document to have footnotes at the bottom rather than inline links.
     * @see http://www.roughtype.com/archives/2010/05/experiments_in.php
     *
     * @return void
    **/
    addFootnotes: function(articleContent) {
        var footnotesWrapper = document.getElementById('readability-footnotes'),
            articleFootnotes = document.getElementById('readability-footnotes-list');
        
        if(!footnotesWrapper) {
            footnotesWrapper               = document.createElement("DIV");
            footnotesWrapper.id            = 'readability-footnotes';
            footnotesWrapper.innerHTML     = '<h3>References</h3>';
            footnotesWrapper.style.display = 'none'; /* Until we know we have footnotes, don't show the references block. */
            
            articleFootnotes    = document.createElement('ol');
            articleFootnotes.id = 'readability-footnotes-list';
            
            footnotesWrapper.appendChild(articleFootnotes);
    
            var readFooter = document.getElementById('readFooter');
            
            if(readFooter) {
                readFooter.parentNode.insertBefore(footnotesWrapper, readFooter);
            }
        }

        var articleLinks = articleContent.getElementsByTagName('a');
        var linkCount    = articleFootnotes.getElementsByTagName('li').length;
        for (var i = 0; i < articleLinks.length; i++)
        {
            var articleLink  = articleLinks[i],
                footnoteLink = articleLink.cloneNode(true),
                refLink      = document.createElement('a'),
                footnote     = document.createElement('li'),
                linkDomain   = footnoteLink.host ? footnoteLink.host : document.location.host,
                linkText     = readability.getInnerText(articleLink);
            
            if(articleLink.className && articleLink.className.indexOf('readability-DoNotFootnote') !== -1 || linkText.match(readability.regexps.skipFootnoteLink)) {
                continue;
            }
            
            linkCount++;

            /** Add a superscript reference after the article link */
            refLink.href      = '#readabilityFootnoteLink-' + linkCount;
            refLink.innerHTML = '<small><sup>[' + linkCount + ']</sup></small>';
            refLink.className = 'readability-DoNotFootnote';
            try { refLink.style.color = 'inherit'; } catch(e) {} /* IE7 doesn't like inherit. */
            
            if(articleLink.parentNode.lastChild == articleLink) {
                articleLink.parentNode.appendChild(refLink);
            } else {
                articleLink.parentNode.insertBefore(refLink, articleLink.nextSibling);
            }

            articleLink.name        = 'readabilityLink-' + linkCount;
            try { articleLink.style.color = 'inherit'; } catch(e) {} /* IE7 doesn't like inherit. */

            footnote.innerHTML      = "<small><sup><a href='#readabilityLink-" + linkCount + "' title='Jump to Link in Article'>^</a></sup></small> ";

            footnoteLink.innerHTML  = (footnoteLink.title ? footnoteLink.title : linkText);
            footnoteLink.name       = 'readabilityFootnoteLink-' + linkCount;
            
            footnote.appendChild(footnoteLink);
            footnote.innerHTML = footnote.innerHTML + "<small> (" + linkDomain + ")</small>";
            
            articleFootnotes.appendChild(footnote);
        }

        if(linkCount > 0) {
            footnotesWrapper.style.display = 'block';
        }
    },

Optionally list links as footnotes #8

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