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The location of the FBI's Training Academy in Virginia. Scully was both a student and an instructor at Quantico - and it was there as a student that she had a rather intimate teacher-student moment with Agent Jack Willis. Willis reappeared in Lazarus, who according to the 'official line' died in a shootout. Scully was briefly reassigned back to Quantico when The X-Files divison was shut down in The Host and suggested Mulder do the same rather than quit the FBI. (Jennifer) 
A gift to Scully from the decidedly fatalistic psychic Clyde Bruckman in Clyde Bruckman's Final Repose. The Pomeranian (a breed of dog) was originally owned by Bruckmans neighbour, though when she passed away the dog was left without food and was forced to eat his owner's remains to stay alive. Scully named the dog Queequeg, a reference to the cannibal crew member in the classic 'Moby Dick.' Sadly Queequeg met an untimely end (some suspect it was the result of a conspiracy among The X-Files' writing crew) in Quagmire, when it became a bite-size snack for the lake-monster Big Blue. (Gwynne Siak) 
The Mulder's summer house in Rhode Island. Since Mulder's parents split, his mother vowed never to set foot in the summer house again, though in Talitha Cumi, she had a heated argument outside the house with the Cigarette-Smoking Man. Inside the house, and with the help of his mother's jumbled hint of 'palm', Mulder finds an alien stiletto inside a lamp in the summer house. (Calvin Lichty)