I have the same issue. I was hoping that the 4.01 update and the Java update would fix it, but alas no.
Sites that don't work?
Most anything that invokes a JavaScript to open a new window. For example, clicking the Upload a File button in the file section of MobileMe.com The print a shipping label in www.ups.com. The browse to and upload a photo in www.yelp.com. All things that try to open another window on top of the current window. All fail. Click on the button or link and nothing happens. Safari works otherwise. no hang, no error, just no response to endless clicking.
As a clue to tracking this down, I use Speed Download. If I click on a Download Link and Speed Download is not already launched and running, clicking the download link will not launch Speed Download and add the download to the queue. If Speed Download is running, clicking on the download link or icon in Safari will pass the download request to Safari and it will work.
I remain convinced that there is a bug in Safari. Your post reporting the exact same symptoms on a completely different computer confirms that the problem is not with my unique setup but with Safari and how it interacts with Mac computers in a real world environment, where there are third party apps and add-ons. I am sure that this problem doesn't affect everyone and certainly doesn't show up on a "pure vanilla" all Apple installation.
I have NONE of these problems in Firefox, it just works. I will give Safari credit for rendering faster that Firefox, but it I can't click on a link and get it to respond, then the Safari browser is useless. Because there is no work around or menu shortcut or contextual menu that will get it to work.