What are the secretly good computer science colleges/universities?

In my particular area of expertise, Georgia Tech is surprisingly strong. In 3D graphics, Brown and Utah have great programs. Pick a specialty, and usually you can find a top program in that area which isn't one of the usual suspects.

For schools whose reputation/ranking in CS is significantly higher than their overall ranking, Purdue would be high on the list. Several otherwise representative state universities have exceptionally high rankings in CS, including the University of Illinois--Urbana-Champaign, University of Wisconsin--Madison, and the University of Texas--Austin. The most "stealth" top 50 CS school may be North Carolina State University.

Apart from Cornell, none of the Ivies are engineering power houses. However, most of them actually have decent to very good Computer Science programs. Princeton, Columbia, Penn, Brown and Harvard all have great CS departments. I feel like the urban universities like Columbia, Harvard and Penn are improving a lot. Entrepreneurial CS students want to be in metropolitan areas where they can find funding, resources and an active startup community. NYC and to a lesser extent Boston satisfy these requirements. For example, http://dormroomfund.com/ operates in the cities of these universities.