Site integration would be top of my list ... With more and more people creating site-wide communities I think that this area has to be addressed fairly quickly. In addition to any code changes I think that this needs to be accompanied by good documentation.
On the site integration issue, in addition to being able to use the WWWThreads users' database it would be great if we could use the message system. For example, I would like (registered) visitors to be able to post comments about articles, news items, site links, etc. but I would like to be able to do this via threaded discussion. Since WWWThreads provides this I would like to be able to create a new thread for each article and link to that thread from the bottom of each article (maybe including the discussion itself at the bottom of the page). The thread would be in the w3t_Posts table but it would not be visible (or searchable) via the main discussion forum. Effectively I want to create a hidden category containing hidden boards that contain threads relating to web pages linked by some sort of ID number. The threads would only be visible via the 'source' web pages.
One other small thing ... Can we have a configuration setting for where email notifications come from? I would like to be able to set message notification as coming from the defined Webmaster (as currently happens), coming from the recipient (if they reply it goes back to them!) or from the poster (if they reply it goes to the poster). I always forget to hack this bit when I upgrade! It would also be good if this could be set for subscriptions, private message notifications and reply notifications.