I'm trying to work out a way to do this without it being awkward. I think automatically marking all topics as read at the end of a session defeats the purpose of having unread topics marked; either you've read a topic since the last reply or you haven't. However, I could see some users who would want only to see topics that have received a reply since their last visit marked.

I guess it's a question of what the marker means. Does it mean that the topic has had activity that you haven't seen yet, or is it simply a notification that something has occurred since your last visit?

I'll probably roll these two options up into a user preference and let the user determine the behavior.