There is a dconf key that stores the whitelist for Unity’s systray (the thing that shows the ugly green skype icon but doesn’t show your dropbox icon).
To see the current value type:
gsettings get com.canonical.Unity.Panel systray-whitelist
You should get something like: ['JavaEmbeddedFrame', 'Wine', 'Skype']
Now if you, like me, use the Skype plugin for Pidgin you don’t need Skype’s non-mono icon disrupting your dekstop, and if you would like to see what Dropbox is doing (at least I don’t see any indicator support for now…) you can change this key with this command:
gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Wine', 'Dropbox']"
And voila no Skype icon but the dropbox icon is sitting in your tray after your the next login.”
Source - http://www.omgubuntu.co.uk/2011/03/how-to-hide-or-show-app-tray-applets-in-ubuntu-11-04/