The Royal Flush Gang bikers come around a corner while running from the police and later Barry blocks the street with a news van in episode 1x11 "The Sound and the Fury".
Kara arrives downtown to stop Parasite who has reappeared only for Mr. Mxyzptlk to show up to help posing as a superhero in episode 2x13 "Mr. & Mrs. Mxyzptlk".
Scully and Mulder meet up for the first time in awhile and are joined by Tad O'Malley who offers them a ride in episode 10x01 "My Struggle".
The scene of angel Six and Baltar discussing humanity's future was filmed here, disguised as NYC in episodes #419 & #420 "Daybreak". Photos available at The 13th Colony.
When Walter and Peter arrive in Mind New York they see the signal from Olivia here in episode #319 "Lysergic Acid Diethylamide".
Peter arrives in the future in the middle of a street battle in episode 3x21 "The Last Sam Weiss".
Wade races to catch up with the convoy on his stolen scooter as it is fired upon by Cable.
Douglas Pease is caught on camera running a red light in pilot episode.