After upgrading to Snow Leopard and a couple of hours headache, I finally got my custom AMP running again.
These are the problems I encountered and what I had to do to fix them:

1. My Apache configuration files were completely overwritten. I had to recreate my vhost settings under /etc/apache2/extra
2. MySql did not work anymore. I had to download and install the latest dmg image for 10.6 and then copy my databases into the new data directory under /usr/local/mysql-5.1.45-osx10.6-x86_64/data
3. PHP was installed without php.ini and gave warnings about timezone settings – had to copy /usr/local/php5/lib/php.ini-recommended to /etc and set the date.timezone to my local timezone

I found this page quite helpful.