Based on my experience, the MySQL queries seem to be just taking an excessive amount of time to complete. Could be high load/disk I/O, or just the database needing some work. There's always a lot of factors that it could be in these cases. Looking at the HTTP headers, this forum is only running on Apache? Are you guys running anything else for caching?
If not, with a forum this size, you really need it. An OPCODE cache would go a long ways for one. Then, there's also Nginx or Lighttpd which will let you squeeze a lot more performance out of the server.
This is on a dedicated server right?
If you haven't figured it out yet, I do this stuff for a living. I'm system admin by trade. Should you guys need any help, let me know, and I'll be happy to help out. I don't expect you to grant me back end access to the database or anything, but I can give some tips.