When you are in the dark, the normal "Look" command is automatically replaced with a "Touch" command. Click on Sophia for hilarious responses.
At one point in the game, the player is given the chance to pursue one of three mutually exclusive paths, which have been nicknamed "Wits" (with more emphasis on puzzles), "Fists" (with more combat encounters) and "Team" (where Indy continues the adventure with Sophia). The three paths eventually converge in the last act of the game.
The shelf in Indy's office features Easter eggs:
- A Thugee idol from Indiana Jones and the Temple of Doom (1984),
- A purple glowing meteor from Maniac Mansion (1987) (another LucasArts adventure game)
- and letters from Indy's dad to the school board. Indy says they all start off with "Regarding Henry", which refers to the drama film Regarding Henry (1991). which starred Indiana Jones film actor Harrison Ford.
One of the items Omar offers is a baseball he claims is signed by Lou Gehrig, but when Indy examines it he says, "It's signed by some guy named Ron Gilbert". Ron Gilbert is the creator of the Maniac Mansion and Monkey Island series, as well as the SCUMM game engine which most LucasArts adventure games use.
There are references in the game to every Indiana Jones film made at the time of the game's creation:
- Raiders of the Lost Ark (1981) - In the Algerian dig site, there is a depiction of the Ark of the Covenant from on one of the walls (Indy aptly remarks that he has seen that before). The labyrinth on Crete features a giant boulder trap.
- Indiana Jones and the Temple of Doom (1984) - On the shelf in Indy's office at Barnett College, their is a Thugee idol.
- Indiana Jones and the Last Crusade (1989) - In one of the Atlantean chambers, there is a stone cup to which Indy remarks that it is definitely not the cup of a carpenter, a reference to the Holy Grail. There is also a "X marks the spot" on Crete.