Ravael Angeline has a tutorial posted on WP.Tutsplus.com that covers the basics of a header.php file. This particular file is located in every WordPress theme and is essential to how a theme works. Also worthy of reading following the tutorial is a comment by Tom McFarlin.
- Hasty Mistake With WP2.8 Header Design Challenge
- What Do You Need In A Starter Theme?
- Good Guide On Avoiding Theme/Plugin Lock-In