Indiana Jones and the Last Crusade was always my favorite Indy movie, for quite a few reasons:
-Julian Glover as villain!
-Inherently over-the-top conclusion!
-Stunning special effects for the time!
-Weird Nazi book-burning subplot!
But most importantly, it was very very funny (and intentionally funny, unlike Temple of Doom).
And now I know why. According to this terrific bit of information, Tom Stoppard rewrote almost every line of dialogue in the whole movie! (Tom Stoppard is most famous for Rosencrantz and Guildenstern Are Dead (brilliant and hilarious) and for writing the screenplay for Shakespeare In Love (another candidate for criminally overrated, mind you).
He also was invited, along with M. Night Shyamalan, to draft a script for Indiana Jones and the Kingdom of the Crystal Skull, but lost out to David Koepp (screenwriter of Jurassic Park!).