Shit

In a parallel universe, a Time Lord chided a colleague for his language when he reacted to news of the Doctor's escape with the exclamation "Oh, shit!" (AUDIO: Exile)

Cousin Eliza mentioned that the lions in Trafalgar Square "gave [her] the shits." (AUDIO: The Shadow Play)

In a fit of rage, Ianto Jones once lamented, "Like you care. I clean up your shit, no questions asked, and that's the way you like it." (TV: Cyberwoman)

Gwen Cooper described a piece of modern art as shit. (AUDIO: More Than This) She also used the word when she discovered that she needed all of Torchwood Three's members eye prints in order to open the rift. (TV: End of Days)

Kaitlin Russell once exclaimed, "Holy shit," after she and Rhys Williams found a body crushed under plastic. (AUDIO: Sargasso)

Behind the scenes
In COMIC: Assimilation², Jean-Luc Picard and Worf use French and Klingon equivalents of the word "shit", "merde" and "qi'yah" respectively.