At the end of the episode you can see several locations from the past of the MCU on the screen including Vormir, Xandar, and Ego among others.
In Loki's file regarding the destruction of Asgard, the Revengers are noted. The Revengers is the name Thor gives his group that includes himself, Banner, Loki, & Valkyrie in Thor: Ragnarok (2017).
Roxxcart is a reference to the infamous Roxxon Corporation. Roxxon, a corporate front for Hydra, has appeared in various forms in Agent Carter (2015), Daredevil (2015), Iron Man (2008), and even the Thor prequel Marvel One-Shot: A Funny Thing Happened on the Way to Thor's Hammer (2011).
A variant of the God of Mischief in Yellow Jersey, holding a trophy, is meant to represent multiple-time-winner of the Tour de France competition, Lance Armstrong, who later revealed to be cheating on competitions using prohibited performance-enhancement drugs.
At 18:11, there is an obvious "372" behind Loki at the TVA library. This refers to the Thor #372 comic featuring an early appearance of the TVA.