I'm posting this to know if other people had the same problem.
Every 2/3 days or so i get a very high CPU load on my server.
I had no problem with my server for a long time, and since i migrated one of my sites to WPMU, i get this issue, which sometimes creates a HUGE php5/cgi queue and ends up in the server being overloaded.
Therefore i've added some logs to understand the exact time and found out that the WPMU site was causing this. I already cleaned/removed faulty plugins, i have just a few plugins left which don't change many things.
I've found the 1 minute interval where the load gets very high and i found out from mysql binlogs that wordpress was launching many wp_cron at that time, as i see many updates of the cron and _transient_doing_cron of each blog, and many updates of the _site_transient_update_core of the network.
I saw that there were some topics about wp-cron making their server overloaded, however many are old or incomplete.
I think there's somehow a bug in wordpress which makes this wp-cron go in loop or something but it's not an easy task to dig into this problem.
Any feedback or help appreciated!