Cruz says to JJ "We've seen this before. We find her kid, maybe she'll talk." He is referring to the op they worked on in 200 (2014).
One of the reasons Reid fancies the name Ethan, Blake's son, may be because one of his best friend is also called Ethan as he relates in Jones (2007).
The figures Penelope puts on Reid's table are from the long-running BBC series Doctor Who. Specifically, the standing humanoid is the Eleventh Doctor, the reclining humanoid is the Tenth Doctor, and the 2 that look like robots are different versions of the Doctor's arch-enemies, the Daleks.
The building that was used for the exterior shots of Reid's apartment, The Langham, was the same building used for exterior shots of Hotch's own apartment back in Season Five.
