Thanks guys for replying so quickly. As my handle says it I am a complete Newbie on the subject (Capital N).
This is a portion of the article I am talking about. I gather that it is to check your own website, about the server OS and Web server well I don't have a concrete situation, I was just wondering what are the tools in general (I guess that there are many tools to use).

"Taking A Second Look (Webpage Access Logs And Hacker Behavior)
Once again I'm going to use the example of a "webpage hack". Simply because it's the easiest to visualize, it's something that I think most of our users will be familiar with, and it's an area where I'm less worried about "spilling the beans" (hey, I worked hard on this stuff, I deserve to keep secrets, haha).
Behavior, behavior, behavior. I can't say it enough, and I hope that this simple, common sense example, can show you why.
Let's say that www.AntiOnline.com was hacked (God forbid). All of the system logs were gone, and the webpage was changed with a message from some hacker telling what he really thinks of me (You can all envision what and ugly site that would be, haha). I can't come up with any "leads" using other methods, as the hacker has left no "virtual fingerprints" for me to find on my system, or the systems of any of my uplink providers. Or has he?
How many of you have had to investigate a webpage hack, for some reason or another? How many of you have noticed that many of the system logs, which would have given you valuable insights into the hacker's identity, have been deleted? Ok, now, how many of you still had the webpage access logs from that system? I bet almost all of the hands in the room just went up, huh? It's something almost EVERY EVERY EVERY EVERY hacker leaves behind. Why? What damage could it possibly do to them? Well, a lot more than they may think."

Thanks again for the help, I am just trying to learn more about security in general, I am not following a pattern, there are so many good articles and tutorials on AO that I take them one at the time.
JC