Can I accomplish this with CSS?
<a href="something">A</a>
<a href="something_else">B</a>
<a href="something">A</a>
<a href="...">C</a>

body
{
    counter-reset:section;
}

a:before
{
    counter-increment:section;
    content:counter(section)". ";
}

1. A
2. B
3. A
4. C

1. A
2. B
1. A
3. C

a:before
{
   content:attr(data-counter)". ";
}​

var linkcounter = {};
var counter = 0;
$("a").each(function() {
    if (!linkcounter.hasOwnProperty($(this).attr("href"))) {
        counter++;
        linkcounter[$(this).attr("href")] = counter;
    }
    $(this).attr("data-counter", linkcounter[$(this).attr("href")]);
});

var linkcounter = {};
var counter = 0;
var anchors = document.getElementsByTagName('a');
for(var i = 0; i < anchors.length; i++) {
    if (!linkcounter.hasOwnProperty(anchors[i].getAttribute("href"))) {
        counter++;
        linkcounter[anchors[i].getAttribute("href")] = counter;
    }
    anchors[i].setAttribute("data-counter", linkcounter[anchors[i].getAttribute("href")]);
}

http://google.com/
http://google.com
google.com
google.com/
www.google.com

var counter = 0, cache = {};
$('a').each(function (i, a) {
    a = $(a);
    var href = a.attr('href');
    var c = cache[href];
    if (!c) {
        counter++;
        c = counter;
        cache[href] = c;
    }
    a.text(c + '. ' + a.text());
});
​