Those apps are a part of the firmware and were not installed from .deb packaged files. This means that the application manager has no tool with which to uninstall them.

You can do the next best thing and hide them from the launcher screen by entering the following commands as root from your terminal:

cd /usr/share/applications
rm skype.desktop
rm youtube.desktop
rm twitter.desktop

....and so on.

Be aware that these icons will likely re-appear when/if you update your OS when PR 1.2 comes out, but you can just repeat the above commands to hid them again.