Bad Axe Games' Trailblazer

As a quick suggestion, I recommend that anyone interested in game design and mechanics with familiarity with D&D 3E take a look at Bad Axe Games' Trailblazer PDF. The crew at Bad Axe has done a very thorough breakdown of the core mechanics of D&D 3E with a focus on what makes the system tick and why it works. The Trailblazer rule modification guide contains their analysis and suggestions for improving the game. I personally found it to be a useful approach in analyzing other RPG systems (including the MUDs I work on as a hobby) and for $5 it's a great a buy. If you're not interested in dropping any cash, you can also check out this EN World Blog for some more great info from one of the Bad Axe crew.