Mallow (Super Mario RPG: Legend of the Seven Stars)
Storm Talent Fairies (Disney Fairies)
Wizards and Witches (Harry Potter); via Weather-Modifying Charms
The Sea Hag (Charmed) has power over her natural environment. She can create rainstorms, hurricanes, and even tidal waves.
Trisana chandler (Circle of Magic) can use weather magic.
Discord (My Little Pony: Friendship is Magic) can both manipulate and create storm clouds as well as summon clouds made out of cotton candy which rains chocolate milk.
Stormy (Winx Club) is a witch who's been described as the "Queen of Storms" Stormy creates and controls storms, thus deriving a pun from her name. She can create strong gusts of wind. She draws her powers from storms and the wind.
Icy (Winx Club) can cause magical blizzards and snowstorms
Diviners (Wizard 101) are wizards and witches from the School of Storm, their specialties versed around storm magic.
Storm Talent Fairies (Disney Fairies) are able to control the weather and conjure lightning.