Joe and Eddie go to the train station to try and stop Leonard Snart from leaving the city in episode 1x04 "Going Rogue". Joe finds Laura Stone at the train station and warns her about Clive Yorkin in episode 3x12 "Untouchable".
Cisco tracks Dr. Light to the train station and Barry confronts and ultimately captures her in episode 2x05 "The Darkness and the Light".
Station where the train full of dead folks is found and the start of episode #218 "White Tulip".
Fauxlivia tries to pass back over to Over There in episode #308 "Entrada".
Train station where Grant Russo gets off a train in episode 3x09 "Marionette".