The Windows Update Applet covers both Windows Update as well as Microsoft Update. Optional updates such as those for Skype, office, Lync, Windows Defender, Virtual PC, and other MS stuff typically come from Microsoft Update. That is why they are unchecked by default and appear as optional updates. Microsoft Updates appear when the software for which they are applicable is installed; I see updates for Office, Visual Studio, and Skype as optional updates, for example, but I don't see updates for Lync or anything else. Other optional updates include things like the x64 update listed in your screenshot, which only applies to those using Japanese or Korean language IME.
I wasn't able to get the Skype update item to appear on any system on which I had not installed Skype for Desktop, and once I did, the update appeared (since I install a older version). I was thinking perhaps the preinstalled Skype might trigger the Microsoft Update but apparently it doesn't- I had to install Skype for Desktop before it appeared.
I've not yet tried it but it may be the case that the update will still appear after I uninstall Skype as well, if the registry keys hang around.
