After upgrading my Mac OS X Snow Leopard to Mac OS X Lion, I noticed that some of my PHP extensions that I had compiled to work with the Apple PHP 5.3.6 binary had been removed. Some, not all. Which I assume is due to them having been compiled 4-way binary compatible (PowerPC and i386/x86_64). Since Lion no longer supports PowerPC, it seems that all the extension files that had PowerPC in them were removed. Xdebug was still there, but all the rest were gone. Below is the process I performed to get everything back.
Download and install MacPorts 2.0.0 for Mac OS X Lion.
In Terminal, run the following commands. The first one may take a while to update the binaries as it compiles them.
sudo port upgrade outdated sudo port uninstall inactive
Download and install MySQL 5 (currently at mysql-5.5.15-osx10.6-x86_64 as of this writing) for Mac OS X.
You may not need to install MySQL, though I chose to do so as I wanted to update to the 64bit System Preferences panel, since I was running an earlier version of MySQL 5 previously.
I also noticed that my /etc/php.ini file was moved to /etc.php.applesaved and no longer called any of my PHP extensions I had set.
In Terminal, run the following:
sudo cp /etc/php.ini.applesaved /etc/php.ini sudo apachectl graceful