Have you isolated it to be a board thing? IE - if you close the boards for a few minutes, does the server calm down?
What are the most accessed files? Do you have logs running for that? If you can find out what's being used the most, you can work on reducing the load that the particular script does to the server.
A suggestion would be to turn off zlib compression if it is running. It improves speed by compressing files -- the problem is that in high-traffic sites this means that the processor is doing a lot of extra work compressing stuff.
Hope that helps a bit.
