The Sankara Stones were the artifacts Indiana Jones was seeking in Temple of Doom
Zak McKracken drew a map that he saw in a dream with a crayon
The plot of Zak McKracken and the Alien Mindbenders revolved around aliens in disguises
The mask from an African shaman near Kinshasa is from Zak McKracken
The "flakes in San Francisco" are the Society for Ancient Wisdom in Zak McKracken and the Alien Mindbenders, who were looking for crystals to build an alien device
The one thousand year old, or millenium, falcon is a reference to Han Solo's ship in Star Wars
A piece of the slimy purple meteor from Maniac Mansion is in Indy's office
The leather jacket dialog option was parodied countless times by Monkey Island and others.
In the Nazi's art collection within Castle Brunwald, one will find art pieces that also appeared in Maniac Mansion, including "Sunday in the Park" and the nude statue. Indy will say the exact line of dialogue that a teenager from Maniac Mansion would say upon looking at the statue and the plaque on it. The beach scene from Loom can also be seen in the painting on the left.
Henry's home is decorated with the venerable Chuck the Plant, who has appeared in several LucasArts games.
The artifacts in Indy's office include a Sam & Max totem pole as well as replicas of the Sankara stones from Indiana Jones and the Temple of Doom.
Don't forget the bugs from Temple of Doom!
A reference to Professor Abner Ravenwood, Marion's dead father as mentioned in Raiders of the Lost Ark.