Also, the document formatting is a little inaccessible. The submit page should have either a link to the document formatting, or just verbatim contain the document formatting page content. This probably won't help people who have been on HN for a while, but it would definitely be useful to me.
The top navigation is also a little confusing at first; I would expect that "comments" would show only my comments. I did not have an expectation of what "threads" would show.
EDIT: Forgot to put that an explanation of some of the more strange behaviors in FAQ would be nice. For instance sometimes there is a reply button to comments and sometimes there isn't.