It seems that all of the Qt4 based apps do, but they also use and configure cmake to take care of all that automagically.  From what I can tell, Gtk3-quartz support is not as mature as Qt4, and gtk-osx-application development has been uncertain.  I know how to create an OS X application bundle with the icons manually, but I am still researching if this is doable automatically at build.

I used Inkscape to copy the vector paths to the mac Xcode Icon Composer app, which generated the file.  If there is a way to do this at build time, I am not aware of it, but the process is simple enough that any time the reference icons change, I could update the icns files manually.  To be honest, I'm still not sure how to apply the icons to the executables built on OS X, but I figured to just proceed one step at a time.

This same case applies to the Gnumeric icons I submitted earlier today. Admittedly, these are not a high priority change, but I hope to learn how to make both gnome-chemistry-utils and gnumeric into first class citizens on OS X, one step at a time.

I have created Mac OS X .icns files from the supplied pixmaps.  I hope that you will consider adding them to the project.