The uniform worn by the dead 31st Century historian is similar to that worn by Daniels in many episodes.

The 31st Century research vessel is a ship capable of time travel that is bigger on the inside than it is on the outside. The same is true of the TARDIS in "Doctor Who".

Archer wonders what the child of a human and Vulcan would look like.  "He eventually" finds out in the third season episode "EČ".

Mike Sussman revealed that the original episode idea was much different than what made it to screen. Orignally, the story had the Tholians capturing a ship from the future and the Enterprise crew trying to stop them from stealing it's technology. The ship in question would've been the USS Defiant from "The Tholian Web". According to Sussman, that story was scrapped due to (among other things) cost. That storyline eventually was used in the 4th season episodes "In a Mirror Darkly, Part 1" and "In a Mirror, Darkly, Part 2".

Archer initially wonders if the dead pilot is Zefram Cochrane who disappeared several years ago. Of course, what really happened to Cochrane was revealed in the original Star Trek episode "Metamorphosis".