Riften - human waste, stagnant water, rotting fish
Markarth - smoke, human waste
Windhelm - horse, not much else since the snow would freeze everything. Indoors probably of human sweat though
Winterhold - might be a whiff of strange chemicals coming from the College
Solitude - a sickly mix of too many people wearing clashing perfume who may not have taken a bath recently
Morthal - rotting things, typical swamp smells
Falkreath - human sweat, freshly cut wood
Dawnstar - smoke, fish, salt water, but the cold wouldn't make those smells strong
Riverwood - cut wood, human sweat. Actually comes across as one of the cleaner places.
Crypts - rot and stagnant water
Caves - of whatever last died/lived in them
Great Outdoors - varied