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A stake was commonly believed to be one of the only weapons that could kill a Vampire, (WC: Monster File: Vampires) and were often made from wood. (PROSE: Iris Wildthyme and the Unholy Ghost)
History
When the verger wielded a mallet and a wooden stake, he thought of himself like Van Helsing. (PROSE: Iris Wildthyme and the Unholy Ghost)
In River Song's diary, it was noted that it was common belief that stakes could kill Vampires, but she also noted that various myths had become confused. (WC: Monster File: Vampires)
Joanna Harris once gave "Fred the Eternal Snail" the V Factor, and she and her team had intended to keep the snail as a mascot, but Slake trod on him, though the snail didn't die, so Joanna had to stake the snail with a toothpick. (PROSE: Vampire Science)
The Ninth Doctor once carried an ancient Gallifreyan weapon, a sonic stake, while he was on Parvanna. He used it against a creature. (COMIC: Tales of the Dark Times)
Other uses
The Head was quite literally a head on a stake. (AUDIO: Wildthyme at Large)