Do you have any recent fcgi processes die in your error.log?
I wonder if the processes are spawning because they are waiting on mysql. I still have concern over your long queries being over 10 sec. It tells me that those are probably mysql writing a temp table out to disk...and disk tables for a busy server like yours are deadly. (still just a theory...but it would be interesting to see your disk access read/write during those maxcpu times.) This is related to if your website has a lot of fulltext searches.
Are these custom queries or a packaged script?
I would also increase your key_buffer_size to at least 128M and see how it goes. I keep mine the same rough size as my index files. You can reduce it once you solve some problems.