I thought I should let you know about a new application that recently appeared in the iTunes App Store called iMoleBuilder (iTunes link). It is a $12.99 molecular visualizer that also lets you construct molecules and save them to the device or an available FTP site.
It has many of the features that Molecules lacks, including some that I doubt I will ever implement. These include the aforementioned molecular construction tools, the ability to load files from FTP sites (I may borrow that), visualization of surfaces, and generation of carbon nanotube and crystal structures.
The user interface is a little hard to navigate, but such is the problem with complex applications on the iPhone (and why I probably will never add some of the capabilities this has to Molecules). The price could also be a turnoff to some, but you can tell it took some serious effort to implement this. Have we really lowered our price threshold so far that $13 is too much to pay for an application?
Unfortunately, the author's website leaves a lot to be desired, and is all in Korean, so I don't know how serious he is about supporting this application. If I could, I'd like to encourage him to keep up the good work. We certainly need more quality scientific applications like this in the App Store.