I am building a new Windows Server 2008 R2 install to host my Joomla! 1.6 website. What are best practices of hosting a WAMP production server? What should I do for partition? A drive for logs, a drive for the OS and a drive for data? What would be the most ideal and secure setup?
The best practices are not to use it. It's best to pick tools native to your platform. If you want to run an *AMP stack, do it on Linux/Unix and install/configure the components individually, don't use a preconfigured package that's aimed at development.
The default configuration for WAMP/LAMP is extremely insecure, because it's meant to give a quick turnkey dev environment. It's not a production solution. If you really care about security, you'll install each component separately and follow the best practices for security for each product individually.