After installing Skype 4.0 on Ubuntu Precise, I see its indicator in top bar, but there is no running application icon on the left, thus I can't focus into it and pin to the Launcher.
I had 2.2 version before, but purged it as described in Skype 4.0 still looks like 2.2 beta, so I believe this can be considered clean install.
Related question is whether it's possible to have overlay with new/unread messages in the unity launcher icon similar to indicator?
You have to install sni-qt 
package:
If your Ubuntu is 32 bits:
sudo apt-get install sni-qt
Or, if you are using 64 bits:
sudo apt-get install sni-qt:i386
I'm not sure if you need to logout / login afterwards, but Skype will then appear together with other indicators.
Consider the missing launcher a benefit and install skype-wrapper, which integrates Skype nicely into Unity:
sudo add-apt-repository ppa:skype-wrapper/ppa
sudo apt-get update && sudo apt-get install skype-wrapper
See this article for further details: http://www.omgubuntu.co.uk/2012/05/skype-wrapper-adds-call-actions-notification-fixes-ubuntu-12-04-support
I have equal behavior with skype icon. But, after using "apt-get install" from command line to install skype, this problem was resolved.
You should try to install skype using "apt-get install", if it's not that.
More over, this installation method is recomended instead of skype website.
sudo add-apt-repository "deb http://archive.canonical.com/ $(lsb_release -sc) partner"
sudo apt-get update && sudo apt-get install skype
I've found it here:
It's actually back to what it used to be (in early versions of Ubuntu), so you need to 'whitelist' the notification icon.
Take a look at http://www.webupd8.org/2011/04/how-to-re-enable-notification-area.html (or google 'skype whitelist ubuntu'.
