first and foremost i want to say that this is not going to make your server 100% cracker proof, there is always a possibility that somebody will find a way in. I have listed a lot of things you can do to protect your server and that will help you secure it. While securing your server you have to find a median between what is secure and what restricts your clients or websites.
you can easily make your server 100% secure from remote attacks by unplugging the ethernet cable, but chances are you will not get much good with it. this is not a complete guide and i will update it when i find time or it needs it. Overall it is a very good start and it is probably more then most servers have.