Last Crusade was one of the most innovative of the LucasArts adventures. It expanded on LucasArts' traditional adventure game structure by including a flexible point system - the Indy Quotient score - and by allowing the game to be completed in several different ways. When the game was restarted or restored, the total IQ of your previous game was retained. The only way to reach the maximum IQ of 800 was by finding alternative solutions to puzzles, such as fighting a guard instead of avoiding him.
Indiana Jones and the Last Crusade: The Graphic Adventure also introduced the phrase "Hello, I'm selling these fine leather jackets" which became a running gag in future LucasArts games. The phrase is a reference to an in-house promotion that was going on during the game's production.
All the Swastikas had to be removed from the game prior to its release in Germany. According to Boris Schneider who translated most of the LucasArts adventures, this was a very challenging task, especially with regard to the software that was available to him back then.
In the VGA version, there is a painting in the vault of the Brunwald castle which features a beach that appears as scenery in Loom.
A replica of Henry Jones' Grail diary was included with earlier versions of the game. While very different from the film's version, it provided a collection of background information of Indy's youth and Henry's life, as well as copy protection codes. Later versions of the game came with a much shorter version of the Grail diary which contained only copy protection codes and basic instructions.