I picked "The Last Crusade" for two reasons. One, it's the one I've seen the most number of times, and therefore it is the one I am most familiar with. Two, it has all the perfect elements which set it apart from the other films. It has the best ending, the most incredible quest, and to top it off, a classic actor portraying Indy's dad! WOW!
I haven't seen KOTCS yet, but I doubt it could be a more fitting end than "The Last Crusade".