#1 - Raiders
#2 - LC
#3 - ToD
Raiders has everything a film fan could want. Action, comedy, romance, suspense, plot twists, intelligent plot, great acting, no gimmicks, etc.
LC is a very close second. It has the same elements as Raiders and, if the initial Indy movie didn't exist, LC might be my favorite of all-time.
ToD is third mainly because of Willie. There are times in the movie when she just really annoys me. Now I realize that's part of what her character is supposed to do, but it becomes a negative when it starts to take away from the movie. I'm also not a huge fan of Shorty, but I think he's a quality character. Instead of a big, burly guy like Sallah at his side, Indy has a short, scrawny kid. Nice twist.
The next question to be answered: where will Indy 4 rank on the list?