as a current yale student, I have to say that yale does a terrible job of maintaining its online presence in general. these recent upgrades to the college site and the admissions site are welcome breaths of fresh air in a sea of bad looking webpages and outdated layouts. just take a look at the homepage and compare it to the homepages of other schools in the ivy league - there's definitely something lacking in terms of vibrant graphics, new focus, web 2.0 look, etc. there's one thing to be "traditional" in appearance and another to just simply be backward. facelifts are definitely needed
I concur with whoever mentioned UChicago's new website; it looks great and it's very informative! The only issue I have with it is that in some cases it has, say, two different pages on the same subject that contain different information, and you need to find both to get all the info you need. But this is a common problem with websites that are overloaded with content, like most college sites. I've certainly seen much worse.
Vassar's website is a good one, and Tufts's looks great.
As for Yale's main page... lol. Columbia's also looks slightly outdated, but I think that's mostly down to the color scheme. Deep blue can make any website look old.