To deal with #1 you need to validate all data before processing. I like to use Data::FormValidator for this.

Dealing with #2 is harder. Doing validation early can help, since you won't be doing expensive processing on invalid data. But if someone is really out to get you they can flood you with valid traffic too. I wrote CGI::Application::Plugin::RateLimit to deal with this problem for a CGI::App, but it's only as useful as your ability to distinguish one client from another. This problem can also be dealt with at the network level by your firewall or by something like Apache's mod_throttle.

-sam