It is vitally important for their understanding of chemistry that they understand that molecules are three-dimensional things and that they have a spatial requirement in that they have a shape of their own and that shape will change. They can't do higher level manipulations without an understanding of three-dimensional nature of molecules.
In organic chemistry for anything that's structure-based it’s imperative that they understand molecules are three dimensional - that they have a spatial requirement. And you can talk about the actual real-world outcomes of that, like drug design and penicillin structure and things which might be what they're actually interested in.
Use model kits for third year pericyclic reactions: It's visual and it's used every lesson because everything uses the same rule. That's the message to get to them - that you’re not teaching four new things. It's all the same rules. They just move slightly differently. So they see the same models and they can see where the cyclic reactions close. That's very hard to demonstrate in two dimensions. The bigger models are much better as well.