For this to be useful, I'm assuming you're also using Homebrew for the MySQL and PHP portions of the native AMP stack.
First, I noticed that all my bins, including all Homebrew packages, that were symlinked in usr/local/bin were gone.
Fix for Homebrew packages:
$ brew list -1 | while read line; do brew unlink $line; brew link --force $line; done
Next, I reinstalled the Command Line tools for Atom and Sublime Text.
Then I noticed that my Virtual Hosts stopped working. Luckily, the Mavericks installer made a backup of httpd.conf that we could recover:
$ sudo cp /etc/apache2/httpd.conf.pre-update /etc/apache2/httpd.conf
$ sudo apachectl restart
I then encountered a problem with PHP. Reinstalling with Homebrew was a problem however because of configure: error: Cannot find OpenSSL's <evp.h>.
I was able to resolve by re-installing the latest Command Line Tools for Xcode :
$ xcode-select --install
Turns out Mavericks also nukes your php.ini file. To recover:
$ sudo cp /etc/php.ini-5.2-previous /etc/php.ini
$ sudo apachectl restart