[decklin]

You can communicate with the Skype client over DBus, which allows you to replace a lot (although not all) of the UI with something else. Two examples:

http://code.google.com/p/skype4pidgin/ https://github.com/technomancy/dotfiles/blob/master/bin/skyy...

The protocol is incomplete (the "native" Qt UI isn't built on it), but it is at least documented on their dev site.

[scribu]

There's also https://launchpad.net/~skype-wrapper/+archive/ppa but it's buggy and still requires you have the main Skype window running.