最近のGistの仕様変更に暫定的に対応した。Chrome 12.0.742.91で動作を確認。Operaでは動作を確認していない。

diff_for_gist.user.js

// ==UserScript==
// @name           Diff for gist.github for Chrome
// @namespace      http://ss-o.net/
// @include        https://gist.github.com/*
// ==/UserScript==

(function(){
	var f = function($) {
		var rev = $('#revisions li');
		if(!rev.length || rev.length == 1) return;
		var diffSelect = function(e) {
			var me = e.target;
			var c = $('#revisions li input:checked');
			if(c.length > 2)
				c.each(function(i) { if(c[i] != me) c[i].checked = false; });
			$('#diffExec').attr('disabled', (c.length != 2));
		};
		var diffcontent;
		var files = document.getElementById('files');
		var diffsrc = 'https://raw.github.com/gist/105908/diff.js';
		var diffscript;
		var d = document.createRange();
		d.selectNodeContents(document.body);
		var diffExec = function() {
			if (!window.Diff && !diffscript) {
				var script = diffscript = document.createElement('script');
				script.type = 'text/javascript';
				script.onload = diffExec;
				script.src  = diffsrc;
				document.body.appendChild(script);
				return;
			}
			if(!diffcontent) {
				diffcontent = $('#files div.file')[0].cloneNode(true);
			}
			var pres = diffcontent.getElementsByTagName('pre');
			pres[0].parentNode.replaceChild(pres[0].cloneNode(false),pres[0]);
			pres[1].parentNode.replaceChild(pres[1].cloneNode(false),pres[1]);
			files.insertBefore(diffcontent,files.firstChild);
			$(diffcontent).hide();
			var selected = $('#revisions').find('input:checkbox:checked');
			var link = selected.map(function() {return this.value});
			var desc = selected.map(function() { return $(this).parent().text().replace(/\s+/g, ' '); });
			var req = function(url,func){
				var x = new XMLHttpRequest();
				x.onload = function(){
					files.appendChild(d.createContextualFragment(x.responseText).querySelector('.file')).style.position = 'fixed';
					func();
				};
				x.open('GET',url,false);
				x.send(null);
			};
			var dif = function(){
				setTimeout(function(){
					var pre = $(pres[1]);
					var udiff = new UnifiedDiff(
						document.querySelector('.file:last-child div > pre').innerText,
						document.querySelector('.file:nth-last-child(2) div > pre').innerText,
						4
					).toString();
					udiff = '--- ' + desc[1] + '\n' + '+++ ' + desc[0] + '\n' + pre.text(udiff).html();
					var len = udiff.split(/\n/).length;
					if(len < 5000) {
						udiff = udiff.replace(/^(\+.*)$/mg, '<span class="gd">$1</span>')
							.replace(/^(\-.*)$/mg, '<span class="gi">$1</span>')
							.replace(/^(\@.*)$/mg, '<span class="gu">$1</span>')
							.replace(/^(.*)\n/mg, '<div class="line">$1</div>');
						pres[0].innerHTML = new Array(len-1).join(',').split(',').map(function(a,i){return '<span>'+(1+i)+'</span>'}).join('\n');
					}
					pre.html(udiff);
					$(diffcontent).slideDown('normal');
				},100);
			};
			req(link[0], function(){
				req(link[1] ,dif);
			});
		};
		var button = document.createElement('button');
		button.name = button.id = 'diffExec';
		button.textContent = 'Compare';
		button.onclick = diffExec;
		button.disabled = true;
		$('#revisions')[0].appendChild(button);
		rev.each(function() {
			var check = document.createElement('input');
			check.type = 'checkbox';
			check.name = 'diff';
			check.value = this.querySelector('a.id').href;
			check.onclick = diffSelect;
			this.insertBefore(check, this.firstChild);
		});
	};
	var script = document.createElement('script');
	script.type = 'text/javascript';
	script.textContent = '(' + f.toString() + ')(jQuery);';
	document.body.appendChild(script);
})();