But it's also possible that artists (and especially designers) tend to use it a lot just because they've heard that it's beautiful, when really it's nothing special. In this case, it would just tend to crop up in beautiful works because a) it crops up in all kinds of works anyway (base rate) and b) there's a whole lot of looking for it in hindsight (especially in works acknowledged as beautiful, while nobody goes looking for it in ugly works).
Some kind of A-B study would be nice. I found one (http://www.livescience.com/7389-sense-beauty-partly-innate-s...), but the methodology seems a bit lacking, I'd say it's far from conclusive.
Thing is that the ideal might not be the golden ratio. Maybe we prefer pi/2 instead of (1 + sqrt(5)) / 2. Who's to say? Pi/2 is if anything -more- fundamental. It seems to be that we don't like things to look too square or too oblong, which limits us to the range of 4:3 through 7:3 as 'aesthetically acceptible'. phi just happens to be in the middle of this. So is pi/2, as noted previously.
You could test this, by showing people some rectangles and asking which ones they like -- 1.4:1, 1.5:1, 1.6:1, 1.7:1, 1.8:1, 1.9:1, etc.
One thing that's interesting is the rise of 8:5 screen dimensions over the old styles of 4:3 and 16:9. 8:5 is, coincidentally, right next to phi, and is in fact a convergent of its continued fraction. 8:5 includes 1280x800, 1440x900, and 1680x1050, 4:3 includes 640x480 and 1024x768, and 16:9 includes the oddball 1366x768. It could just be that the math is easier with 8 and 5, though, since their reciprocals both terminate.
For example, being right or left handed doesn't seem to have any particular advantage, as long as your handedness is the same as everyone else. It seems like humans have arbitrarily "chosen" right-handedness. :)