[cd34]

When it happens, ssh into the server and do:

free
iostat 5 5
vmstat 5 5
uptime
uname -a
ps ax | wc -l
ps ax | grep -Ei '(apache|httpd)'|wc -l

and post those.

Is the site doing anything dynamic? i.e. some php script that is calling the database? if so, check your slow-query log around the same time as the events happen.

Its also possible that the server is bogged down with DNS requests since you mention it happens when urchin is running. Log files could be overly large causing slowdowns. Many different possibilities.