From pilot episode.
From episode 1x10 "The Woman at the Airport".
From episode 2x17 "The Priest in the Churchyard".
From episode 4x01 "The Yanks in the U.K.".
Brennan and Booth travel to LA and the trail leads them to this rooftop pool in episode 1x10 "The Woman at the Airport".
Sweets is in a subway wreck at the start of the episode. Check out the Earthquake ride portion in this video. in episode 5x15 "The Bones on the Blue Line".