mcmcom:
There are some things that you just shouldn't do. Like, trying to teach 8 year olds how to safely handle a live cobra... or drive an automobile.
I'm not calling you an 8 year old. I'm just saying that you should definitely not be securing a web server by yourself. You should spend some money to hire a consultant for 8-10 hours to secure your server - or maybe walk you though doing it yourself.
MarkR is right: There's nothing you can do to the server that will protect you against the inexperienced programmers who work for your company. All you can do is get them some training or fire them.
The most dangerous thing about this thread is that when people try to answer your question, it suggests that it's a question that is answerable.
Turning on Safe mode won't make you safe.
Reading a two year old Sitepoint article won't make you safe.
Turning off a few flags at the suggestion of some anonymous people in an online forum won't make you safe.
Get about 5 years experience installing IIS and Apache web servers, write some complex programs and learn how to defeat the security of the code you've written. Hire some good people who already have some experience.
The most dangerous thing about following some helpful little "checklist" of things that will supposedly make you secure is that it makes you falsely think you're secure when you're not. The converse of that is that it's better to be insecure and know it than to think you're secure when you're not.