Here’s what’s bugging me about the OP’s question: He (or she) is not really asking what colleges resemble Williams, they’re asking whether there are specific universities that, though they have almost nothing in common with Williams other than the presence of the occasional honors college or an esteemed college of arts and science (that derive their reputations from the presence of a graduate faculty) nevertheless share the same kind and sort of prestige? In the middle-ages, this would have been called alchemy. They are two different elements.
LACs derive their prestige from their resemblance to English public schools, with ample playing fields, grassy quads and a kind of secret society access to different levers of power within The Establishment. It was not without some justification that the late lawyer and diplomat, John McCloy, an Amherst graduate, was often referred to as the “Chairman of the Board” of the Establishment. Wesleyan’s Henry Wriston (Class of 1911), Williams’ Phineas Baxter and others, were cut from the same cloth. They all seemed to have served with or had some connection with the OSS during The War and the CIA afterward.
The post-Sputnik modern university movement, with the possible exception of HYP, basically eschewed all of that stuff in favor of an entrepreneurial approach to science and technology and the so-called, “production of knowledge” which no LAC can compete with on a literal level but which they can exploit to a great extent by recruiting brainy STEM-oriented kids who like working in small, cooperative environments with a lot of mentoring.
For the above reasons, people who like one type of campus, don’t usually like the other; but, in today’s environment where generous financial aid has become a confounding factor, I am not surprised that many, many people need to cover all bases. Using a ranking system is just not the way to do it. Figuring out possible “overlaps” is one way that is fairly legitimate, IMO.