Molecules can be classified based on the number of atoms they contain (monoatomic, diatomic, triatomic, polyatomic), the type of atoms (homoatomic containing the same type vs heteratomic containing different types), and their size (micro molecules are small while macromolecules are large, containing thousands of atoms). Common examples of different types of molecules include diatomic molecules like O2 and N2, heteratomic triatomic molecules like H2O and CO2, and macromolecules like proteins.