Gnome-Do is one of most useful features installed on my system. But I hate how big the Docky's default icon size was.
So here's the easy way to resize it (the less easy way is to tweak the gconf-editor):

• to resize the bar length : hover your mouse over the bar's side until you see resize icon, drag left-right to resize,
• to resize the icons : hover your mouse ove the vertical separator on the left hand side of clock applet, drag up-down to resize

At first, I looked for its configuration on Gnome-do preferences but I couldn't find any.  I even tweak the gconf-editor! And must restart the gnome-do to see the effect.
I was thinking, because it is Linux I must do it the "text way"  :)
You did too?

update (thanks Sander):
For those who like the geekier way, here's how :

• run gconf-editor either by press Alt-F2 and type gconf-editor, or click the shortcut on System Tools -> Configuration Editor,
• go to /apps/gnome-do/preferences/Docky/Utilities/DockPreferences/IconSize and change it to your desired size number,
• quit gnome-do, and then start gnome do,
  
• enjoy
  

keyword : gnome-do, docky, resize icon,