I agree with anag&lit on the above point - it can be irritating to post a comment on, say, "Clue Chain" and then have to navigate back through the pages to get to where you were posting from.
Already discussed, but the single most irritating thing is then I am using my laptop, the reply box by default appears just where the pop-up adverts are - many is the time when I have activated the advert instead of typed a post! (Less of a problem on the desktop, as it is set to show a bigger screen area)