Check out http://security.stackexchange.com/ for this type of question.
You need to think in terms of two types of security: Overall OS security for the L part of your LAMP stack, and application security, or the AMP part of the stack.
For overall system security you can try OSSIM to do some basic tests, but there is definitely a learning curve.
Each Wordpress and Drupal install (depending on the amount of privilege you give administrators of each site) is a potential liability with third-party plugins and the like. Take a look at this question for some great pointers.