Game Design References
Luckily in this day and age we get the privilege of learning from some of the great masters of Game Design. I'm going to attempt to compile a huge list of articles I've found.
Pixel Prospector has some excellent broad coverage on game design in this list
There is a decent article on Gamasutra on Modular level design.
He does a great job explaining how you can use excel to help design modular levels with interconnected rooms. It gets much more complex when you think of applying it to graph theory and 3d level design, but the visual with the Carcassonne tiles really helps illustrate how it might be really cool to apply to procedually generated 2D levels.
Patrick Wyatt is an awesome man who not only worked on the original Warcraft and Starcraft games, but also went on to found Arenanet and launch the first version of Guild Wars. The man has been pure gold when it comes to setting up small game studios into huge juggernaunts. His blog on Code of Honor is pretty enlightening.
Here is a great reference on designing UI systems to make sense to the player.