Include Files

If you've used server side includes or PHP includes you are already familiar with the idea of including files within files for content that is common to multiple pages. WordPress uses some standard PHP includes and of course you could also add your own. These are the most commonly used include files.

header.php
header.php includes typical header information such as your doctype, meta elements and stylesheets, as well as some things specific to making WordPress function. If you want you could end this right before <body <?php body_class(); ?>>, but most people will also use header to include their banner and primary navigation menu. It's helpful to include body_class if you want to use conditional styling. When you have that in your header, WordPress will add additional classes to the body which you can use to style things differently on different pages. That's how I've incorporated different background images in the banner for different sections. Another option would be to use different header files for different sections in which case you would give them unique names.
sidebar.php
sidebar.php can be used to include code to automatically generate menus, manually coded menus, code to include widgets and other elements. You can also use multiple side bars, as I've done on this site, if you don't want the same information on every page.
footer.php
footer.php is where you put your typical footer information. You can also add code to include footer widgets here if so desired.
searchform.php
searchform.php includes the standard code to incorporate a search form in your site. It can be customized to suit your needs. I usually include it in the sidebar.
comments.php
comments.php includes both the code for people to submit comments and the code to display them. It is usually included in single.php using <?php comments_template(); ?> though there may be times when you might also want to include comments on a regular page.