A couple things I've noticed. The first one. Looking at your mysql_slow_query_log there are a couple of things that are really hitting MySQL hard. One is an old query from your w3t_Posts table, looks like a query on an old version that people are still getting to and running. It looks something like:
SELECT B_Number
FROM w3t_Posts
WHERE B_Approved = 'yes'
AND B_Status <> 'M'
AND B_Board IN ('board1','board2','etc')
AND B_PosterId = 'userid'
When that query runs, it's taking anywhere from 10-90 seconds from looking at the slow query log. So it looks like you have an older version that people are still going to and this query is executing.
The second slow query is one that I had noted earlier, and that's the option to show the total # of new posts. With the number of forums you have, including subforums, this is another query that is pretty slow. The reason being, is it appears that many of your users never visit some of the forums, so the number of new posts in some of them continue to grow. Even though they never visit them, that query is executing for every forum every time they visit the main page. There's no way to really optimize this, it's a resource hog and always has been, which is why it's noted that way in the control panel.
I can't say these are the reasons you're seeing the very high load average, but the slow query log has about 3 weeks of data i n it, and it has about 4000 entries. Meaning over the course of that time, there have been 4000 queries that have taken over 10 seconds to execute. And they all are the queries I mentioned above.
