It seems to me that you have at least three classes of judgement in your question. 1. Prejudice. 2. Common Sense. 3. Informal definitions. 4. Inductive generalisation.
Let's start with the latter: if all the Xs I have come across are Ys, and if I have no reason to believe that the Xs I have come across are exceptional or otherwise not representative, then I have some confidence that Xs are Ys. Americans are foolish.
What I am calling an informal definition is a way of describing an identifying feature of something: dogs have four paws. Now, this is different from the above because you very likely learned about dogs in part by having the number of paws pointed out to you, whereas probably you didn't learn what an American is by having their foolishness pointed out.
Continuing backwards, I would claim that the first two categories have something social or cultural about them, that the second two do not necessarily have. Common sense is called 'common' to indicate that it belongs to a particular social group at a particular time. What is common sense to an 18th Century French farmer is a very different set of beliefs than common sense to a Google employee in 2015. Prejudice is similar.
However, if we wanted to attempt to differentiate between common sense and prejudice, we might start with the following. First, common sense usually means something positive (a good thing, tending to be accurate), whereas prejudice something negative (a bad thing and a mistake). However, insisting on that difference would beg the question. Further, common sense can be quite practical (particular ways of doing things, such as how to store grain, for the farmer; or good practice in coding software), whereas the things we call prejudices do not. Again, prejudice is value-laden towards its object ("any application written by Microsoft will be rubbish"; people from X are lazy and criminal) whereas common sense, where it is value laden, tends to be so towards the person who claims or denies it ("he has no common sense"). Finally, prejudices tend to form a system (someone who is prejudiced against nationality X is likely to be so towards other nationalities), whereas common sense does not. This may have something to do with why prejudice is more difficult to change than some specific bit of common sense: common sense resists new evidence to be sure, but yields more easily than prejudice because of this systematic quality.