On 64bit Ubuntu systems, Skype uses the Clearlooks theme instead of the default Ubuntu theme, Ambiance (this also happens with other themes).
This occurs because Skype is a 32bit application and the GTK2 theme engine (Murrine or Pixmap in most cases) is not installed for 32bit.
Here's a screenshot with Skype on 64bit Ubuntu systems without the fix:
And here's Skype on the same Ubuntu 64bit system, after fixing the theming issue:
To fix this Skype theming issue in Ubuntu 64bit, all you need to do is install the 32bit Murrine GTK2 engine as well as the Pixmap GTK2 engine (in case you're using a Pixmap-based GTK2 theme):
sudo apt-get install gtk2-engines-murrine:i386 gtk2-engines-pixbuf:i386
For Ubuntu 12.04 and 12.10, you'll also have to install the ia32-libs package (at least, that's the way I got Skype to look properly in my test under Ubuntu 12.04):
sudo apt-get install ia32-libs
And finally, restart Skype.