Bill,
The two files which you need be most concerned about are: 1. /opt/local/etc/my.cnfThis file is not provided by default by mysql5. Have a look at the sample my.cnf files in /opt/local/share/mysql5/mysql/ and pick one according to your liking (mine, for example, is my-small.cnf with "#skip-networking" uncommented).
In mine, I have "socket = /opt/local/var/run/mysql5/mysqld.sock" in both the [client] and [mysqld] sections, which is, as Paul said, the standard MacPorts socket location.
2. /opt/local/etc/php.iniHere, I have "mysql.default_socket =" in the [MySQL] section and "mysqli.default_socket =" in the [mysqli] section. An empty value means that it will check my.cnf's [client] section.
As for the difference in the directories, the logic on the mysql developers' part is that the more-standard lib, bin, etc. aren't theirs to mess around with, but rather the package managers. The logic on our part is, well, we are the package managers :)
What are your permissions on /opt/local/var/run/mysql5 ? On my system, this directory is 755 mysql:mysql, since that's where the socket resides.
Chris
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