I know what the projects are about: Safari is Apples browser. WebKit is the engine used in Safari (and in many other browsers) which is open source. The WebKit source code contains also code to compile it as a standalone application. You can download the nightly build of WebKit here: http://nightly.webkit.org/
I have compared some of those nightly builds of WebKit to the official Safari application. And besides the slightly different logo and the different name, I haven't really seen any difference.
Are there any? Or is it just the branding?
Edit: I just tried again with the current nightly build of today and it even names itself "Safari" now.
The WebKit nightly builds only contain changes in the render engine, but don't change the UI at all. If you install the WebKit nightly build you get a newer version of the WebKit render engine, which is faster and more advanced as the older WebKit render engine shipped with Apple's Safari. For example if you visite www.html5test.com with Safari and the WebKit nightly build, you'll see that the WebKit nightly build scores more points because it has newest version of WebKit and therefor has even more advanced html5/css3 etc. support than the WebKit build used in Safari.
The UI that is used in the WebKit nightly builds is exactly the same as in the current version of Safari. As the UI is not part of the WebKit render engine, no changes are made to it by the WebKit devs. The browser vendors (Google, Apple etc.) build and publish the UI.
