Ok thanks. I installed LiteSpeed to do a test. And it seems its PHP that is the problem. Since Litespeed builds the same PHP you had before and the load is somehow reduce but it did not improve.
That means my PHP build is the problem. About the scripts and sites, I dont think that is possible, they are not custom PHP scripts but pretty standard run on every webhosts, wordpress, phpbb, smf, etc. None of them are high traffic, but the load sometimes just goes crazy and with "top -c" its shows "Php" as taking more resources.
So LiteSpeed did no helped allot, but at least I know PHP is now the problem. I do have a little suspicious but Easy Apache did not warned me about. When I compiled Apache I use suPHP without memcache or anything else because I was not sure if those are standard, I only selected eAcelerator. So the build runs fine. But I readed somewhere that suPHP doesnt support any kind of caching, that includes eAcelerator. Is this truth?
That means every PHP is generated from 0 instead of having it cached, which could explain why with so little requests the load gets so high. An Admin told me its MySQL but the strange is that MySQL is not on Top of high cpu usage, its always php proccess, and not a specific one, but from several users.