The specifics are the clearer divs (or at least most of them) are definitely going. Where possible they will get removed by structuring things to render them unnecessary. In other cases it's a question of experimenting to find out what works best. I am beginning to favour the "overflow:hidden" method of containing floats, but we will have to see.
I think most of the <div class="inbox"> will go as well, nobody has used them for styling and the IE problems they were designed to fix can be dealt with in other ways. Viewtopic looks like it's in for a facelift to simplify styling it. It might also be possible to scrap one layer of divs from the forms.
The downside is the more standards compliant PunBB becomes the harder it becomes to integrate with old sites. Put PunBB in the middle of a site which is also XHTML Strict (or even transitional) and things are fine. Try and integrate it with some antique DW Template and all hell breaks loose.