By using Advanced Configuration Editor in Gnome, you have access to some Docky properties not listed in the preferences, like the option to change Docky’s position on the desktop.
Press Alt+F2, enter: gconf-editor and in this configuration editor, navigate to “apps -> docky-2 -> Docky -> Interface -> DockPreferences -> Dock1” (this sequence is in my system). On the right side there are some properties with their corresponding values, including the position of the dock which you can change from “Bottom” to “Top/Left/Right” to move Docky to the upper part of the desktop.
N.B. “Left” or “Right” may not work in some versions (I do not know those versions).
Any changes made do not apply until you restart GNOME Do.
The above works for my system.
Ubuntu 11.04 – the Natty Narwhal