Company smell is where no-one really cares about developing software, where the company allows ridiculous concerns to get in the way of good practices, where you won't learn anything from anyone. Companies with Company Smell can have good software, good interviews, even pass most of the Joel test, but you get inside and everything's slightly off.
One of the most obvious smells is when people think they're agile because they are cargo-culting some aspect... Features are on index cards, or they hold a standup once a week. It's an almost physical pain when you're in this situation and you know Agile can work, you have experience that it's better and people all around you are either dismissing it offhand or only pretending.
Obviously it's helpful to be able to detect company smell before starting at a company, but how do you develop that sense? What are some indicators during an interview that the company you're applying for smells, and how do you go about calming any fears?
(Edit 201118011259 - Changed Title)