Scott knew about Gerard Argent's cancer because he smelled the disease off him in Abomination. Isaac Lahey also picks up the debilitating illness in a sick dog, osteo carcoma in Battlefield. Scott affirms that terminal illnesses have a very distinct scent.
In Riddled, Derek Hale explains chemo-signals to Scott that a werewolf can pick up in so to identify emotion. In Lunatic, Scott was able to smell the jealousy off of Jackson Whittemore when they're made co-captains because of the onset of the full moon. In Formality, Peter Hale also warns Stiles that "deception has a particularly acrid scent".
Like their hearing, and voices, werewolves are particularly cued to the scent of their own kind. In The Benefactor, Scott using his sense of smell determined DeMarco Montana was a werewolf, and could also tell he was part of a Pack.