The most controversial new feature of Safari 4 was the placement of tabs on the top of the Safari browser window instead of below the bookmarks bar. At first, I was against this new UI quirk, but the more I used the Safari 4 Beta the more I liked the placement of the tabs on top of the window. Sadly, in the shipping version of Safari 4 tabs have returned to their traditional place.
The other feature that got some people's knickers in a twist was Safari 4's progress bar--or lack thereof. Safari 3 would show a blue bar that filled up the address bar as a page loaded, whereas the Safari 4 beta used the same progress indicator that Mobile Safari uses on the iPhone: a small whirling circle in the rightmost part of the address bar. Safari 4 (non-beta) employs a fusion of the two: the whirling icon is still there, but a solid indicator appears as a webpage is loading that says 'Loading...' just so you know.
You'll also notice that the RSS button that appears on some sites has gone from a nice blue hue to a metallic color that matches the coloring of the Safari window itself (in the image Safari 4 beta is on the left, final is on the right).
These are just a few of the surface details that I've noticed are different during my first few minutes with Safari 4. I'm sure there are more to discover.