Wooden nickels were first a token used at state fairs and similar events. They could be used like currency at the fair, and often in the nearby towns as long as the fair was going on -- after that, when there was no chance to redeem them, they became worthless. Hence the saying "Don't take any wooden nickels." Since then, similar wooden tokens have been used as souvenirs and advertisements.

In 1933, after the failure of a local bank in Blaine, Washington, U.S., during the Great Depression, left the area with a shortage of coins, wooden nickels were actually issued as everyday currency. These round wooden coins were much larger than the metal nickel coin, but were printed with a face value of five cents.

A Google search reveals that there seem to be more establishments (farms, stores, etc.) called "The Wooden Nickel" than any other use of the phrase now. The Wooden Nickel on Fletcher Avenue in Tampa, Florida, is the one I am personally familiar with; it's a costume/novelty/smoking/etc. shop much frequented by people from the nearby University of South Florida.

Sources:
http://www.wooden-nickel.com/history/
http://www.coins-of-panama.com/wooden.html