The "Order of the Stone" is an Easter egg of Minecraft, since Notch was originally going to call Minecraft Minecraft: The Order of the Stone.
If you look at Lukas' hair, his hair style is Lucas' from Mother 3.
Episode 2 was released exactly 1 day after the season disc was officially released.
In episode 7, "Access Denied", with Jesse using the transmigrational headset and is controlling a zombie, he/she digs up the sand. After he/she finishes digging it up, he/she says, "I don't like sand. Stuff gets everywhere." That sentence sounds similar to Anakin Skywalker in "Star Wars: Attack Of The Clones", when he is assigned to protect Senator Padmé Amidala on Naboo: "I don't like sand. It's coarse, rough and irritating, and it gets everywhere."
While exploring the Order Of The Stone's temple, Olivia asks, "Where do these stairs go?" Jesse looks over and he/she has three different responses. One of them is "They go up." If you select that one, it will be similar to the scene in "Ghostbusters" when they go to rescue Dana Barrett and Louis Tully and confront Gozer, Dr. Raymond Stantz asks where the stairs go, and Dr. Peter Venkman replies, "They go up," and they advance to the roof of the apartment building.