MIT also (18.014 and 18.024, see http://student.mit.edu/catalog/m18a.html ).
Note that Harvard has three levels of honors sophomore level math: 23, 25, 55 (the regular version is 21); see http://www.math.harvard.edu/pamphlets/freshmenguide.html .
Then you have Caltech and Harvey Mudd, whose calculus courses would be considered honors courses at every other school.