The incident between Gibbs' father and the German fighter pilot refers to an incident that actually happened in WWII when the German fighter pilot Lt. Franz Stigler escorted a badly damaged B-17 out of German airspace so it could safely return to England.
A bit of hidden humor out in plain sight. The 'body of the week' in this episode is named SGT Michael Dawson. The photo shown of SGT Dawson is of an actor by the name of Wolfgang Bodison, who posed for the image during the movie A Few Good Men (1992), when he played the role of Lance CPL Harold Dawson.
Dinozzo's joke about McGee watching too many Bette Midler movies might be a nod at the fact that Sean Murray portrayed young Thackery Binx in Hocus Pocus (1993) with Bette Midler.
In planning their trip to Eden, NC to see Walter Beck, the German pilot that turned Jethro Gibbs' father, Jackson Gibbs around, Jackson mentions going through Washington DC. The NCIS headquarters is in Quantico, Virginia and Washington, DC is north of Quantico. Eden, NC is barely south of the NC-VA border. It would be pointless to drive north to DC then south to NC.