While this is no means an exhaustive list it is a point of reference for what tags to consider allowing on a website that allows user contributions in html.

<a> <em> <strong> <cite> <code> <ul> <ol> <li> <dl> <dt> <dd> <h1> <h2> <h3> <h4> <h5> <h6> <b> <i> <tt> <big> <small> <ins> <del> <blockquote> <q> <img> <pre> <table> <tr> <th> <td> <p> <br>

I really like Markdown but I've grown tired of a couple of it's problems. Mostly I get annoyed with using underscores for emphasis/italics. Underscores come up in web addresses and in text describing code and computer operations all the time and with Markdown I often find myself having italics where I wouldn't want it. Now it's possible that there are some bugs in the parser but it's also possible that the syntax is correct. I think if I had to make a proposal for a better system would I would use much of Markdown but have the following syntactical additions/changes:
**bold** __underline__ ++ins++ --del-- //italics//