There are some page transition effects that are new as well. Not sure what browser you need to be using to see them, but I'm using Safari.

When I load the "Mac" section, the icons for the various models of Mac sort of spring outwards to fill the scroll area.

Clicking on any of the other categories on that page (like Applications, Accessories, etc. result in a offloading of old icons + reloading of the new category icons that includes the same spring/jiggle.

Also, when I go back to a previous page, like the main page, the navigation bar animatedly drops down from nowhere on page load.

Different color menu bar, far more animations (which have a tightly sprung attitude instead of the previous more smooth transitions), the background color went more neutral grey, the background was augmented by a gradiential noise pattern, there's more of an emphasis on rounded corners...

It's a lot of minor details leading to a pretty tangible cosmetic effect. Also the scripts seem a lot more responsive on my iPad.

(edit: s/w/a/ ugh)

The page background color is different as well. It was white before, now its #F2F2F2.

The new top-level menu looks nice, too, but somehow it just doesn't look "Apple" to me. Maybe I'm just too used to the old site...

I agree with that. I have seen apple.com a few times when I want to drool and this seems strikingly similar. But one thing is, when you have such a minimalistic design, the change in menu bar is a major change.