The Nettuts site has posted a detailed guide to the "comments.php" file that comes with every release of WordPress:

WordPress seems to be everywhere these days, and it's no wonder with it's ease of use and ease of customization. In this tutorial, I'll be dissecting the default WordPress theme's comments.php structure and giving you various snippets of code to make your skinning easier.

The guide breaks down the major parts of the file - some of the general code, how it displays comments, the comment submission form and some "little tricks" it does to handle things like comment numbers, links and the alternating colors.