Smack Down, Gust, Twister, Sky Uppercut, and Thunder (Credit to pikamaster555)
Also, Hurricane. (Credit to Umbrae)
Also, if you have a Pokemon with No Guard, you can hit a Flying Pokemon with any move.
Also, if you use Lock-On or Mind Reader right before they Fly, it will allow you to hit them during flight. (Credit to DarkTyphlosion)