What would be a comprehensive but safe set of html tags to use with the HTML Filter but compatible Markdown?
&lt;p&gt;&lt;table&gt;&lt;thead&gt;&lt;tr&gt;&lt;th&gt;


But you don't need enable all of it, just simple reorder the filters, and put the markdown filter under the html filter. So the html filter will drop the unavailable tags, before the markdown process the text, and build own html.

Edit:
Checked the OpenAtrium's dedicated Markdown filter, it has the following in HTML

&lt;div&gt; &lt;span&gt; &lt;br&gt; &lt;a&gt; &lt;em&gt; &lt;strong&gt; &lt;cite&gt; &lt;code&gt; &lt;strike&gt; &lt;ul&gt; &lt;ol&gt; &lt;li&gt; &lt;dl&gt; &lt;dt&gt; &lt;dd&gt;
 &lt;img&gt; &lt;blockquote&gt; &lt;p&gt; &lt;pre&gt; &lt;h1&gt; &lt;h2&gt; &lt;h3&gt; &lt;h4&gt; &lt;h5&gt; &lt;h6&gt; &lt;table&gt; &lt;caption&gt; 
&lt;thead&gt; &lt;th&gt; &lt;td&gt; &lt;tr&gt; &lt;sup&gt; &lt;sub&gt;


Markdown PHP Version: 1.0.1n
Markdown Extra Version: 1.2.4

And own filter weights: