How can I obscure what I am using to run my site? Is there anything I can do to prevent somebody from knowing my site is using Drupal by looking at the source code of the front page? I am referring to people who scan sites using software that detects the software used to run the website to be able to attack it using any known weak point.

If it is not possible to completely hide the fact that the site is using Drupal, is it at least possible to confuse them (e.g., by aliasing the node pages with URLs like http://example.com/servlets/&lt;node-id&gt;.jsp)?
You can't hide it completely. Most of what's needed to do it, would require hacking core. The biggest tell, is the Drupal JavaScript variable which is readable from the front page, or any page for that matter.

If you want to improve your sites security by hiding that it's a Drupal site, your effort is better spent on code reviews than it is on trying to hide the fact that the site is made with Drupal.