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The Silurians' molecular disperser could convert nuclear energy into microwave rays which could disperse the molecules of the Van Allen Belt. The Silurians were capable of controlling the process in order to ensure it did not go out of control and thus destroy the Earth. (TV: Doctor Who and the Silurians)
A MASER was a microwave weapon that disseminated even subatomic particles, including gravitons, quarks and tau mesons. The Valeyard built one in the Matrix, with the aim of killing everyone watching it. (TV: The Ultimate Foe)
Microwaves could be used to cook or reheat food, typically in microwave ovens. (TV: Resolution) The Tenth Doctor made a DNA detector that was supposed to go "ding!" in the presence of a Zygon, but didn't know when to stop himself, giving it the ability to microwave frozen dinners from up to twenty feet as well. (TV: The Day of the Doctor)