Asshole Victim: Neeva, presuming that she was indeed shot and killed by Jannik.
Call-Back: To the Ancient Communication Device, even referencing the events of ''Avalon, Part II'' where Daniel Jackson and Vala switched minds/bodies with two people on a planet that worshiped the Ori. This also, incidentally, makes this the only mention of Vala outside of SG-1.
The climax of "Origin" — where Mithcell and Teal'c's used the SGC Gate to destroy their Communications Device — is also brought up when Sheppard and Rodney are trying to figure out how to do the same on their end.
Not Right in the Bed: One clue to McKay that it's not really Keller is her suggestion to take the jumper out for a sex picnic.
Production Foreshadowing: The reintroduction of the Ancient Communications Stones is arguably one for Stargate Universe. At this point, it had been 3 years since the last on-screen appearance of the technology. Stagate Universe was in pre-production at this point and would go on to heavily utilize the Stones (or at least an Earth reverse-engineered model). So having the Stones pop up here and now on Atlantis was arguably to help remind the audience who'd forgotten about the technology in advance of Universe.
The Mirror Shows Your True Self: Neeva-in-Keller's-body appears to the audience as Neeva, and vice versa, except for an establishing moment in which Neeva-in-Keller's-body looks in a mirror and sees Keller's face looking back.
The Unreveal: The episode never reveals the fate of Neeva and Jannik, although the viewers do get a final shot of Jannik cocking the pistol and then a gun shot is heard as the scene cuts away, so it implies that Jannick does kill her.
