Chuck Versus the Helicopter - S1-E2
Trivia: During the test where Chuck is shown a series of images, he mentions an "Oceanic flight" that was shot down. "Oceanic" is the name given to many ill-fated fictional airlines, and has been used in films like "Executive Decision" and TV shows like "Lost".
Chuck Versus the Truth - S1-E8
Trivia: When Reardon Paine gets shot in the knee, he yells a Wilhelm scream.