Two things in the current output would need to be refreshed for HTML5. Here's what need to be done:
I'd like to fix these two before we get out of beta in the lib branch.
Regarding the footnotes, this is how I addressed it in Python-Markdown. See the commit message for an explanation.
@waylan class=footnote-ref and class=footnote-backref are indeed better. I forgot that HTML5 also restricted allowable values for the rel attribute.
Lib branch updated to use footnote-ref and footnote-backref classes in the output. a0724cd
Lib branch will keep using the align attribute for table cells, unless the user has set a class himself through the parser's configuration. This way with a default style sheet things will be aligned correctly and you'll still be able to affect the style though CSS using a selector matching it (td[align="right"]); using a style="text-align:right" attribute would make that difficult.