Molecular Assembly Program I'm not totally sure which Stack Exchange community this would go in, but Chemistry seemed best.
I've been thinking for a long time now, that it would be cool to have a program where you could design your own atomic models, from the sub-atomic scale and up, then test them in a real situation. You could create anything from simple molecular structures to...anything.
I've looked around online, but there aren't any programs that you can build your own atomic structure. Anyone know if there are any out there like this?

EDIT: I've tried a few other programs, including Avogadro, this, and another one by PHET.
You  might want to try BioVia's (formerly Accelrys) Discovery Studio Visualizer. This is free software and the "gateway drug" to their sophisticated suite of molecular modeling and chem/bio informatics software. It is a step above the various drawing programs out there and lets the user generate realistic 3-D models of an infinite variety of chemical structures. http://accelrys.com/products/discovery-studio/visualization-download.php