In biochemistry, intercalation is the insertion of molecules between the bases of DNA. This process is used as a method for analyzing DNA and it is also the basis of certain kinds of poisoning.
Clathrates are chemical substances consisting of a lattice that traps or contains molecules.  Usually, clathrate compounds are polymeric and completely envelop the guest molecule.   Inclusion compounds are often molecules, whereas clathrates are typically polymeric.  Intercalation compounds are not 3-dimensional, unlike clathrate compounds. According to IUPAC, clathrates are "Inclusion compounds in which the guest molecule is in a cage formed by the host molecule or by a lattice of host molecules."