Rock

Rock, or stone, was a naturally occurring aggregate of minerals.

Petrification was the process in which organic matter was turned into stone. The hand of Eldrad was petrified (TV: The Hand of Fear) as were Mrs Pritchard and her daughter, Gwendoline, after Light made them so. (TV: Ghost Light)

The Fourth Doctor once expressed exuberance at having landed in a location surrounded by rocks. To demonstrate the cause of the stalemate of the Dalek-Movellan War, he and Romana played a game involving hand shapes forming "stone", "paper" and "scissors"; stone was represented by a closed fist. (TV: Destiny of the Daleks)

The Eleventh Doctor later did the same thing. (GAME: The Eternity Clock)

On the planet P7E, rock was mined for processing. It eventually became an edible substance. (TV: Underworld)

On the planet Nebulax 4, rocks could be squeezed to produce a variety of bodily fluids, such as blood, mucus, saliva, phlegm or vomit, thus rendering the phrase "you can't get blood out of a stone" void. (TV: The Bounty Hunter)

Weeping Angels, when observed, literally turned to stone, as a defence system, using a mechanism known as quantum-locking. (TV: Blink)

There were stone steps in a square in Prague outside a club. (PROSE: Have You Seen This Man?)

Missy's Master TARDIS was swallowed by a space creature, which caused it to grow to the size of a minor planet and turn to stone. Damaged, the TARDIS experienced dimensional leakage and released artron radiation. Using clone slaves, Missy dug through the rock to get to the TARDIS. (AUDIO: The Belly of the Beast)

As a weapon
The ancient Egyptians used rocks as weapons when the Daleks landed in Egypt in search of the taranium core for the Time Destructor. One Dalek was rendered immobile as rocks were piled around its base. (TV: The Daleks' Master Plan) The Red Dalek Leader commanding the mission was killed after it was bombarded by rocks, losing its gunstick and sustaining critical damage to its casing before being buried. (PROSE: The Mutation of Time)

On one planet, the Second Doctor, John and Gillian were able to destroy some Daleks by dropping rocks on them from a high outcrop. (COMIC: Attack of the Daleks)

As part of the Dalek Project, bronze Daleks engaged primitive men armed with rocks. (COMIC: The Dalek Project)

Other references
Singing The Riddle Song, Bliss recited the line "I gave my love a cherry, it had no stone." (TV: Love & Monsters, PROSE: The Time Traveller's Almanac)