I think comments are where the action is. Three simple things that get most of the bang of markdown IMO: Working permalinks for comments, paragraph dividers and clickable links.
There should be a page which lists the submissions that have recently been commented on. Otherwise, it's essentially meaningless to make thoughtful comments on old threads.
Having a *hide* option would be welcome too.
For the time being, I'd settle for just converting newlines to br's. Adding hyperlinks before there's solid infrastructure for dealing with spam would be a mistake. I'll be surprised if more than few days go by before spam shows up, even without hyperlinks.