I guess thats you have a problem with I/O Bandwidth or in other words, the harddisk speed is too slow. I've seen this problem several times with vps servers when too many vps are on the same host system. This can also affect mysql performance. I guess there is not much that you can do about this except of talking with your hosting provider.
What you can try to optimize mysql;
If your sites dont use innodb, then you should consider to switch innodb off in my.cnf file, so that mysql uses less memory.
but then why does Zen Cart and phpbb running with a big DB load pages sub 200ms?
Most likely they cache the results better.