Currently, I can change themes and icons through the Appearance dialog, but this leaves things like the Skype, Dropbox, and Firestarter icons in the notification area unchanged. Where are these stored? How do I change them?
It really depends on the application. The Skype icon is unchangeable. There is an experimental version of Dropbox that you can change the icon on. You might be able to change the Firestarter icon, but you'd probably have to rebuild from source.