Donald P. Bellisario make two cameos, both in season two. First, in Hometown Hero (2005) he is seen outside Abby's lab, tying his shoe. The second appearance is in SWAK (2005), where he is seen in the hospital when Gibbs is interviewing the "rape" victim. In both cases, Gibbs gives Bellasario a quizzical look.
In Hometown Hero (2005), the video seen at the end of DiNozzo's car being crashed into the back of a semi truck is actual footage from a police chase that took place in Buckeye, AZ.
All the pill bottles in Emmy Poole's medicine cabinet with readable labels are for vicodin and prescribed by Yuzo, DDS spanning several years.
The concept of ki that Jimmy Palmer mentions to Abby is the Japanese pronunciation of qi (alternatively chi), which is the Chinese pronunciation.
Alicia Coppola reprises her role as Lieutenant Commander Faith Coleman from JAG (1995). She will go on to play a different character, FBI Agent Lisa Rand, on NCIS: Los Angeles (2009), which is part of the same universe as this series and JAG.