Firefox 4.0.1上のGreasemonkey 0.9.3、Scriptish 0.1で動作を確認した。Chrome 11.0.696.60ではfaviconを置き換えられないようで動作せず。

ldr_favicon_hack.user.js

// ==UserScript==
// @name           ldr favicon hack
// @namespace      http://d.hatena.ne.jp/javascripter/
// @include        http://reader.livedoor.com/reader/
// ==/UserScript==

document.getElementById('total_unread_count').addEventListener('DOMAttrModified', function () {
    var canvas = document.createElement('canvas'),
        ctx = canvas.getContext('2d'),
        unread = unsafeWindow.subs.model.get_unread_count().toString(),
        h = document.head,
        favicon = h.querySelector('[rel*="icon"]');
    canvas.width = canvas.height = 16;
    ctx.font = 22 + unread.length * -4 + 'px sans-serif';
    ctx.fillText(unread, 0, 13);
    favicon.href = canvas.toDataURL();
    h.appendChild(favicon);
}, false);