Alex Cho Snyder in this excellent article describes how he helped design FoldIt a protein folding game.
He mentions the use of Skill Chains from this article. Skill Chains are basically a flowchart of the different skills a player encounters and must master to progress through the game. With respect to educational games, it is a great way to map the educational goals to the gameplay. In the past we’ve generally used tables of skills and how they map into the game. The flow-chart nature of skill chains is superior to tables because the tables imply a linear progression through the skills. Games however are usually not linear and the skill-chains show that.
Scott Brodie in writes Gamasutra about creating more meaning in games by using life experience, distilling it to a core truth, and building your game around that. Brodie applies this idea for making games more fun, but it could be used to make games more educational as well such as mathematics or problem solving.
I love adages (waste not, want not) and here is a huge list of adages for game designers. It was started by Hal Barwood who I met at LucasArts many years ago and Noah Falstein who worked there before my time.
GameCareer.com has an article by Lindsay Grace in Educational Fantasy. This articles explores the idea of the fantasy setting and its necessary role in creating an engaging and entertaining experience. “[Fantasy] is probably one of the greatest single challenges facing educational game design. How can the practical matters of education intersect the enveloping fantasy we expect from games?” The examples of Logo, Oregon Trail and Fantasy Football reminds the reader that educational messages are more exciting in an enhanced and engrossing setting.