flash - embedded sound - video that automatically loads in - unprofessional sites that go off on huge rants about politics or religion or some other topic that is sure to offend a good number of people. Sometimes authors don't seem to get that their author pages are their "professional image" and they need to act professionally. Visitors are not your friends to gossip to, they are your customers.
I saw one once where the post of the day was when the author was in a hospital waiting room and was a multi-paragraph rant on how all the other people sitting in chairs weren't dressed up pretty enough for her delicate senses.
I wince when I see those things - save that for personal blogs and personal facebook pages.
But by far my biggest pet peeve
Not being able to easily find listings of all books and series books in order - yes with easily click-able buy links.