First, this Geekdad idea is great!  I have two boys, 10 and 6, and I've resigned myself to the label of 'geek' or something analogous.  As I get used to posting under my own name and not a snarky and ironic acronym accompanied by a portrait of an 80's robot, I think this will be a good place to exchange stories and ideas. 

So, first post.  My sons are both homeschooled.  My oldest is both gifted and has Asperger's, so public school was not working.  They are both thriving being homeschooled by mom, going through a curriculum that introduces writing and reading through historical studies and literature.  They are now studying waterwheel-era factories and as an illustration of the era, we used Minecraft yesterday with the Better than Wolves mod to allow him to replicate a factory.  He had to lay out the design, explain what it was used for, and then create it in Minecraft.

Minecraft mods have really opened up the game.  We played the 'stock' Minecraft, an open-world sandbox game that allows the creation of worlds through placing of cubes of various materials, since alpha, but at my son's insistence, I learned to install various mods that create new functions.  Better than Wolves mod adds waterwheels, axles, windmills and other interesting elements to the Minecraft game that really fit with the lesson.

Modding Minecraft seems a bit intimidating at first, as it involves finding a java .jar file and using 7-zip or some other utility to actually replace bits of the compiled java code.  Many mods require that other mods be installed first before they work, and some of the more complex have multiple dependencies, each of which has to be found, updated, and must be compatible with the most recent Minecraft version, which is always updating.

That said, the tireless modders have extended the original game to whole new interesting areas, and in our case, allowed us to use it as an educational tool that I'm sure will stick with him longer than simply reading about it in a book.  Just watch out for the Creepers...