Clarke wakes up in the City of Light after taking the chip in episode 3x16 "Perverse Instantiation: Part Two".
Mulder hides out of sight as the pursuer drives past in episode 11x01 "My Struggle III".
Sam Flynn rides his bike up a ramp in the middle of downtown after escaping the cop.
Parking garage ramp seen in episode #109 "Tigh Me Up, Tigh Me Down" and in the opening credits.
Source: BSG Season 1 Location Guide