Presenting an overview of all multi-atom systems is not easy. The reason is that a. there exist many different atoms, b. there exist many different electron orbits and c. the number of possible combinations increases with the number of atoms involved. The combination of these aspects causes a bewildering variety of three-dimensional configurations of multi-atomary systems.
Although there are hardly limits to what is possible, there are limitations in what can be made at a certain stage in evolution.
As long as the earth is a chemical system, the complexity of multi-atoms is limited by what physical chemistry allows, including for example: inorganic molecules, crystals, metal, simple organic molecules, fullerenes.
As soon as cells arise, new types of multi-atoms come into existence, for example lignin, DNA, progesterone, large amino-acids such as are involved in the Na/K pump in the cell membrane, etc.
With the emergence of memons, another leap is made in the configuration spaces of the multi-atoms. Not only can memons create multi-atoms that mimic natural examples, such as artificial flavour, or represent altered versions of natural molecules, such as genetically modified DNA, they can also create configurations that show a purely memic design. Examples are the metal parts of a car (lumps of iron-multi-atom in the shape of whatever part you design), plastics, silicone, non-natural fullerenes, specially designed multi-atoms used in nanotechnology, artificially evolved pharmaceutical molecules, etc.
http://images.google.com/imgres?imgurl=www.csm.ornl.gov/SC98/viz/orbits.jpg&imgrefurl=http://www.csm.ornl.gov/SC98/viz/viz2.html&h=911&w=967&prev=/images%3Fq%3D%2B%2522electron%2Borbits%2522%26svnum%3D10%26hl%3Dnl%26lr%3D%26ie%3DUTF-8%26sa%3DN%26as_qdr%3Dall (beautiful pictures of man-made multiatoms used in nanotechnology)
http://www.ccdc.cam.ac.uk/prods/csd/csd.html (an example of one of the databases in which data on structure of the many millionths of molecules is stored).
http://www.rcsb.org (a large library of proteins)
http://ndbserver.rutgers.edu/ (nucleic acid database)