Argh, I hate the term intelligent molecules (pet hate of mine, up there with sticking 'nano' in front of everything). I am assuming you mean responsive.
I work in polymers, and some of my colleagues work on responsive polymers using fluorescence and UV. A fluorophore and quencher are added during the polymerisation, and changes in the chain structure can be identified as the fluorophore and quencher move closer together or further apart on exposure to a stimulus. Still on polymers: agents can be trapped within a network, and then with e.g an increase in pH the agent is released which can be measured and used to infer changes in the network structure.