This is the episode where Timothy McGee gets promoted to being a full time NCIS Field Agent reporting to Gibbs.
The scene of the agents pulling in to the abandoned train yard is the same exact shot from season 1 episode 17 reused.
If you look at the Webcam on top of the Captain's monitor you'll see the "Logitech" logo is backwards (it's a mirrored image).
Tony says they found fingerprints on Sandy's "hair thingies" Gibbs corrects him calling them barrettes. This is the first indication we have of Gibbs having had a daughter at one point.