I've done this by adding unread class to unread forums and unread topics by applying
<!-- IF forumrow.S_UNREAD_FORUM --> unread<!-- ENDIF -->and
<!-- IF topicrow.S_UNREAD_TOPIC --> unread<!-- ENDIF -->to forumlist_body and viewforum_body templates.
The thing works, but not entirely as it should. What I have noticed is that in 3.2 clicking on "mark forums read" is handled by ajax.js file and by clicking on the "mark read" link does not change the color of unread posts and topics to read (the same way as it does with icons). The unread color changes however, if I refresh the page.
So, looks like I'm gonna have to add or change something in ajax.js file. Anyone here who is willing to help, as I'm not qute familiar with .js? Thanks!