The latest issue of Creative Screenwriting has an interview with David Koepp, the guy who finally did the new Indiana Jones script up right.
I liked a lot of what this gentleman said. At one point he mentions that there aren't any specific one-liners that relate back to the other films, because who remembers something glib they said 25 years ago? He also said that the references to the other films will be played down, because they have to be taken as three in a lifetime of probably hundreds of adventures.
In another rag I read that a mid-30s draft of an Indy script was called "Indiana Jones and the Monkey King" and had our hero riding rhinos to battle a Chinese deity in the search for a magical peach tree. Other rejects include "Indiana Jones and the Saucer Men from Mars" and "Sons of Darkness," about a search for Noah's Ark (which, if my nerdiness serves me correctly, was the plotline of an Indy book [yep, it was: "Indiana Jones and the Genesis Deluge" by Rob MacGregor"]).