WPDesigner has a detailed tutorial series on many of the aspects of putting together a WordPress site template. Here are the lessons he’s covered so far:

#1 Intro
#2 Template Files and Templates
#3 Starting Index.php
#4 Header Template
#4b Header Template Continues
#5 The Loop
#5b The Content
#5c Postmetadata
#5d Else, Post ID, Link Title
#5e Posts Nav Link
#6 Sidebar (and Categories)
#6b Page-Link Listing (wp_list_pages)
#6cGet Archives and Links
#6d Search Form and Calendar
#6e Widgetizing Sidebar
#7 Footer

WPDesigner WordPress Tutorial Series>>