25/30 drupal and i/o problems :-)
Drupal 7 makes some really intensive usage of a bad file_scan_directory function.
Check this drupal bug for example or this and that.
The problem for you is 25/30 websites but all of them are managed by the same apache processes. So it is quite hard to isolate the real problematic drupal instance from the system monitoring tools.
With advanced mode for apache status you could check which Virtualhost is currently running on which apache process (if the long request is long enough for you to catch it). You could also use various calls to lsof command to identify which of the apache children is parsing the disk, and what directories are implied (that would give you the drupal instance). Of course it will be easier with one virtualhost for each Drupal (no multisite drupal deployment).
Now you should at least track the response time of each website, using nagios with check_http, or munin, or one of all the various monitoring tools and web services available. Note that for most of these http monitoring tools the most important parameter is to indicate the server IP and DNS, so that the 25 or 30 different websites are really checked, and not only the first one (default virtualhost). If they all respond in the same time chances are that you forgot to tell the monitor tool the right DNS to use on that http request.
Having the response time for all the websites you will see after any upgrades if one of the drupal instance as lost 1s in the average response time (for example) and this one will be the right target for a deeper analysis.