I use this jQuery Markdown from arhpreston for my purposes, My jQuery code (although not relevant):
var converter = new Markdown.Converter();
$(document).ready(function(e) {
$('#content').html( converter.makeHtml($('#content').text()) );
});
Where #content- div:
<div id="content">This is another of most common type of error. It is usually encountered when you are trying something which needs a user registration(at the very least). If you haven't registered on the hub yet, **Gods help you!**.
Anyways, the hub is mostly open for registrations on weekends(*generally* Sunday; sometimes Saturday too). Keep looking at the **Hub Topic** for the notifying information on the registration details.
### NOTE
You must not, under any non-dire circumstance ask any Admin to get your nick registered. We *WILL* be banning you. It is annoying if nothing else.</div>
Everything is working fine and I have no problems. The only thing that the text is parsed as semi-HTML in Internet Explorer, as shown in the screenshot:

MS IE sucks as usual
As you can see in the screenshot, all my strengths and italics are processed with correct HTML, but all other markups fail. Links (using the scheme [1]:) are analyzed, but not related to the actual content. They are simply added at the end as text.
The following content in between hrshows how it should be analyzed.
. , -, ( ). , !.
, ( , ). Hub Topic .
, , . . , .
IE 7 . IE 8. jQuery - 1.9.1. (Opera, Firefox, Chrome, Safari) (Windows Xp 8, * nix Leopard). , IE , - . , ?