These notifications are created by Growl.
You don't need to install it to get them (at least in newer Growl versions). Since Growl was recently added to the Mac App Store as a commercial application, they'd otherwise scare off the developers responsible for its success (by supporting it). They state:
[...] Growl itself is no longer required in order to display a notification. The 1.3 SDK allows for applications to generate Growl notifications without Growl installed. This is called "Mist" and is a new feature of the 1.3 SDK. Thus, Growl becomes the "pro" version of Growl when allowing you to customize the notifications, and the "free" version is the built-in notification.
Skype uses Growl (apparently in an older version though) to generate its notifications, and so does your Twitter client: