Scully and Mulder watch Tooms where he is being held in a mental hospital in episode 1x03 "Squeeze".
Mulder and Scully enter a secure psychiatric facility to question Eve 6 about the cloning program in episode 1x11 "Eve".
The hospital where Rodney and his sister were held in S4E9 episode Miller's Crossing. From episode 4x09 "Miller's Crossing".
From episode 3x06 "The Real World".