<p>Overall reputation (and more specifically, things like endowment per student, full-time faculty per student in the most popular departments, spending per student, research expenditure per student, % of class who are NMSC National Merit Scholars, and other variables that vary ENORMOUSLY from one college to another, yet aren't often so clear from the "rankings") should be more important factors than the particular department reputation. You should generally speaking go to "the best school you can get into."</p>
<p>I would still look into department reputation, of course, but keep in mind that the rankings are often heavily biased towards the schools with the largest -- not necessarily the best -- programs. To use just one example, Purdue often comes up near the top of engineering rankings because it has such a large department with so many students. I call this the "McDonald's Effect": McDonald's is well known, but in terms of quality it's not #1, even in french fries. But when you look at quality-based rankings, which measure the quality of faculty and students, schools like Princeton, Yale, Caltech, and Rice are at the top while Purdue is way down the list. A better way to look at department reputation is to talk extensively with students and faculty in that department, see where students go after they graduate, and look at the true student to faculty ratios by calculating them yourself for a single department. Also, sit in on a few classes. Again, don't base anything on what you "hear" about such and such's CS, etc., or what the rankings show you. In many cases, the "overall reputation" is a much more accurate picture of the quality of undergraduate education in a department than any individual department ranking you can find. Also, remember than more than half of people switch majors while in college.</p>
<p>Beyond that, also go for "fit" - if you aren't happy, you're not going to take advantage of college to the fullest. But again, don't limit yourself to what you "hear," or limit yourself to schools that fall within a particular category (urban, <2,000 students, etc.) because you'll be overlooking a lot. Visit a bunch of schools for 2-3 days each, including a weekend day, sit in on tons of classes at each and really try to figure out what you like or dislike. I wouldn't say "fit" is more important than overall academic quality, given the enormous variation in quality between the top schools and the "lesser" tiers, e.g., the enormous gap in undergrad educational quality between say HYP/MIT/Amherst and Northwestern/UPenn/JHU/Columbia/Tufts, but it is very important.</p>