On their Easy Peasy Chemistry and Physics page I found links to these fun interactive helpful tools!
At Molecularium we played in the Nanolab. There you could build molecules, zoom in to see their size, and check them out in the different states of matter.
Then at Learn.Genetics we found a cool tool that lets you get a feel for the real size and scale of a cell. Use the scroll bar along the bottom to keep zooming in. It's really cool!
We followed up with this video showing the size by continuing to look at things that are 1,000 times smaller than the object we are looking at. The music is just background and has no context, so we muted it as we watched.
It's really hard to wrap your head around how really tiny an atom is, but these sure do help give us some perspective.