Here is a list of links I found helpful for making the transition from Drupal 5 to Drupal 6:
General
Drupal 6 Release Notes
Converting 5.x modules to 6.x
API reference
Drupal 5.x to 6.x FormAPI changes
Theming
Drupal 6 Theme Guide
Converting 5.x themes to 6.x
Anatomy of a Drupal theme
Overriding themable output
Preprocess functions
Working with template suggestions
Core templates and suggestions