Yeah, I like all the films in their own way, and I agree that TOD is the darkest in tone (human sacrifice, blood drinking etc.). However for me there's something special about Raiders; it has an eerie, otherworldly quality that none of the other films quite managed to capture IMO.
I feel the same way about the original Ghostbusters - it has a special unsettling atmosphere that really enhances the film. I think that the soundtrack has something to do with it.
It's hard to put into words but for me, genre material is often strongest when it succeeds on more than one level e.g. Ghostbusters is a great supernatural comedy partly because it is genuinely eerie; Raiders is a great popcorn adventure film partly because it has this underlying seriousness.