Julius comforting David after the failed attempt to nuke the Invaders's ships.
Steve and Jasmine's wedding, made extra heartwarming by David and Connie fully reconciling.
President Whitmore and General Grey's trust in each other to the point of occasional First Name Basis.
The farewell scene before Steve and David attempt to infiltrate the mothership. Especially the exchange between David and Julius:
Julius: (hands David a pair of airsickness bags) "Here. Just in case."
David: (hands Julius a yamukel and prayerbook) "Here. Just in case."
Julius: "...I'm very proud of you."
In the special edition, David tries to find Connie's private cell number. He tries numerous variations and nicknames, but it doesn't come up. Julius suggests searching for "Levinson," even though she didn't take his name when they were married. David types it in to prove he's wrong...and sure enough, "Connie Levinson" appears.