Some flavors can be only bought in certain areas in Japan (28 different kind) and others are only available during a certain period (3 different kind). Also for only purchasing a special KitKat flavor was invented
Here are some examples:

KitKat with Zunda flavor, made of green beans and a popular flavor for people in Tohoku Area (North Eastern Japan). Additionally 10 yen from each purchase of this KitKat is going to be donated.

KitKat with Wasabi flavor, which is only available in Shizuoka and Kanto(greater Tokyo) area.

KitKat with Kobe Pudding flavor. Only available in Kobe area.

KitKat Shinshu Apple, only available in Shinshu area (around Nagano)

Pakkana series (three different designs: Circus, Party and Piano black). Each contains 20 small pieces (10 regular flavor and 10 with a little bitter taste)
Some other examples are: Apple Vinegar, Bubblegum, Caramel and Salt, Cucumber, European Cheese...(see http://en.wikipedia.org/wiki/Kit_Kat for more)
Enjoy the summer,
Edda