After some searching on the net, I couldn't find anything that told me where to look for php.ini to change this setting. However, when I ran the phpinfo() command, in the output it shows that the php.ini is loaded from /etc, and not /usr/local/, like the sites I found describing the same problem.
So to properly set up your PHP environment, you can copy another php.ini to /etc or copy the /etc/php.ini.default to /etc/php.ini and edit the file accordingly. After you're done, restart Apache to have the settings take effect.
[robg adds: This one bit me, too -- PHP recommends register_globals be set to off, so Apple did the right thing by setting it that way. However, many scripts, such as Geeklog!, require register_globals to be on. If it's off, Geeklog appears to mostly work, but it stops loading pages after the header. It took me a bit of digging to figure out the php.ini location, so hopefully this hint will help some others in the same boat.]

