And also the kind of film stock used has technical reasons. Super 35 film stock is cheaper to use and shoot with than using anamorphic lenses, it also makes the camera lighter to move around, and that is why some director's use that instead of anamorphic. Another thing with super 35 is that it does allow them to use open matte framing for the eventual morons who dont want the film in its original aspect ratio. It is stuff the director never intended for you to see, but it is visible on the pan and scan version all the same. It all breaks down to HOW it was filmed if there is the possibility to have more picture in a 16:9 framed version. But even with opening up the frame, it throws off the careful balance the cinematographer achieved while framing for the INTENDED aspect ratio.
As for picking a wider format over another, it sometimes goes back to purely artistic reasons. Sam Raimi shot a lot of his films in 1.85, but chose to shoot For Love of the Game in 2.35, mainly because he is a baseball nut and wanted to see baseball on the big screen in cinemascope. As others mentioned before, with Spider Man 2 he chose to use 2.35 because that way he could fit MORE of Doc Ock on screen than he could in 1.85.
With Jurassic Park III, Joe Johnston shot it in 1.85 for a few reasons. First is so that it matched with the first two films, even though Johnston prefers to shoot in 2.35. The other is that way the frame is smaller, allowing the dinosaurs to appear larger in the frame. If he had the extra space on the sides, the dinosaurs would not look as imposing.
Ridley Scott shoots in 2.35 most of the time, but shot Hannibal in 1.85 to match Silence of the Lambs.
So sometimes they shoot wide for technical reasons, sometimes for artistic. Just imagine the chariot race in Ben Hur in anything less than its original width. The sheer size and impact of the scene is lost when anything is cut out. Open up the top then the objects of interest become smaller in the frame, thus destroying the focus of the picture.