According to HowStuffWorks, there have been actual, recorded instances of raining frogs. The phenomenon has occurred due to waterspouts, which are whirlwinds that pick up water and aquatic creatures along with that water. The storm carries the frogs to land, where eventually the clouds release the water and the frogs.
Frogs are by no means the only strange things to fall from the sky. However, due to the presence of raining frogs in Exodus, they have tended to receive more attention. According to a Library of Congress webpage, tornadic waterspouts have also deposited fish, stones and salt on land. Notable modern instances of frog rains include Kansas City in 1973 and Odzaci, Serbia in 2005.