As part of my day job I maintain Drug Discovery Resources a website intended to act as a resource for scientists undertaking drug discovery. One part of the site has a section on bioisosteres including many examples http://www.cambridgemedchemconsulting.com/resources/bioisoteres/ in which the chemical structures are shown with dropped shadows.

I use ChemBioDraw to draw the structures and then save as PNG files with a transparent background. The structures are then dropped onto webpages created using RapidWeaver, within RapidWeaver there is an option to add dropped shadows to images. I was recently asked whether there was any other way to create the same effect and Matt at macosxtips suggested using ImageMagick. This applescript droplet allows you to do so by simply dropping the file.