Actually, we've ascertained that it is not the code or queries that cause this per se, but it is the traffic patterns - human visitors + SE crawlers... at times, there are (natural) traffic bursts and that's when the server starts choking.
apache/mysql - stock distros, with some config tweaks, mainly in my.cnf.
>what happens if you just kill one or the other?
Good call. Actually, restarting just apache does the trick most of the times. What we suspect is, abrupt flooding in http requests causes MySQL to slow down which causes http requests to get queued up and finally choke the service.
