Background:
The individual components of ionic compounds and molecules are so incredibly small we can never hope to see them - or can we?
We may not be able to see atoms, but several computer programs give us the ability to visualize them, through creating three-dimensional representations.
Molecular Explorer
Being able to visualize molecules is one thing, but how about playing with them?
Molecular Explorer is a program made by the Alberta Research Council and is available for a very affordable price from the Alberta Learning Resource Centre. For more information on acquiring the program, see this review page.
So what can Molecular Explorer do? It is extremely adept at displaying basic molecules - through a simple window, or pull down menu, the number of atoms can be dictated and the resulting molecular structure is shown:

But what's really incredible about Molecular Explorer, is that you can actually grab the atoms and pull on them, to see how the bonds react and visualize how the molecule retains its shape of maximum stability. This is demonstrated in the following QuickTime movie:
The Molecular Explorer package also contains excellent Shockwave based tutorials and exercises.
Mac Molecule / PC Molecule
This easy-to-use program, available on both PC and Mac platforms includes many premade molecules that can be viewed and manipulated. Using it is a lot like using a graphics program - you can view the graphic in different ways, change colours, erase or add parts, and zoom in and out:

But the best part is the ability to manipulate the graphic, as shown in the following QuickTime movie:
If you are interested in using or purchasing Mac or PC Molecule, see this review for contact information and prices.
CrystalMaker
CrystalMaker is available only on the Mac platform, but it is a fantastic program for visualizing crystals. You can construct crystals from scratch from atoms, view premade crystals and molecules, and (as with MacMolecule described above), you can manipulate the structures to move them the way you wish:

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