I just realized another example: verbal. Strictly speaking this word means of, or relating, to words, but when we say a verbal contract we mean a spoken agreement rather than a formal, written contract. So the denotation is "related to words" but the connotation is "oral rather than written."

from http://www.m-w.com
Main Entry: verbal
Pronunciation: 'v&r-b&l
Function: adjective
Etymology: Middle French or Late Latin; Middle French, from Late Latin verbalis, from Latin verbum word
Date: 15th century
1 a : of, relating to, or consisting of words <verbal instructions> b : of, relating to, or involving words rather than meaning or substance <a consistency that is merely verbal and scholastic -- B. N. Cardozo> c : consisting of or using words only and not involving action <a verbal protest>
2 : of, relating to, or formed from a verb <a verbal adjective>
3 : spoken rather than written <a verbal contract>