There are many.
A simple example is solubility. Molecules with amines generally are soluble in acid. Molecules with carboxylic acid groups are usually soluble in base. Molecules with flexible hydrocarbon chains tend to be soluble in oils. Molecules with lots of polar groups tend to be soluble in water. Large, rigid molecules are rarely soluble in anything.
Trained chemists can do this sort of thing with specialized properties (such as metabolic stability, brain penetrating ability, and oral bioavailability) as well, although success depends on specifics.