Well I did design documentation and level documentation modules at uni, so I might be able to help. The uni used Capture the Dude as their main template (awful game but maybe it can help you). The full design document can be found here:
http://web.cs.wpi.edu/~id111x/c05/pr...proj1/gdd.html
For a more puzzle based document, search for the grim fandango one - you should still be able to find it out there somewhere. I personally think it's laid out very well.
Also, it's often good to make use of flowcharts and bubble diagrams!