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".
Douglas Pease is caught on camera running a red light in pilot episode.