My bet is that you would smell wood smoke, bread baking, and stew or soup cooking over a fire.
Medieval people were very clean. They believed that cleanliness was next to godliness, and they believed that bad air transmitted disease. So if something smelled bad, they either cleaned it or got rid of it. We have records of people being fined because they left refuse in the street outside their shops. And while they sometimes did have drains that lead from the house to the gutter, the source of the drain in the house was in the kitchen or laundry, and the human waste went elsewhere.
The reputation they have for being smelly seems to come from the Renaissance. One particular passage I have seen referenced several times refers to the use of rushes to cover a floor, and what the rushes covered over was pretty vile. The passage comes from a letter written by Erasmus to a friend, however, and refers to conditions that were current in the late Renaissance. In context, it is pretty clear to me that Erasmus is making a comic comparison between English inns to badly run stables.
There is a link below to the history section of an article on bathing, where there is some discussion of the medieval attitudes toward being clean.
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Medieval towns were crowded because serfs wanted more freedom and moved out of the manor land to towns.
Some medieval towns transportations were wagons or carriages. Some people just walked.
Regulate production or trade ;)
Many medieval towns were clean by their standards, which would have meant uncluttered, without foul odors, and so on. The medieval people did not understand anything about bacteria, viruses, and disease vectors, so in some modern senses, the towns were not clean; for example you could not trust the water.
Grim, smelly, overrun with rats, no sanitation, muddy streets, completely foul, and cities and towns were not a lot better.