I was wondering if these control panels were developed internally for these companies or are they possibly available commercially?

Does anyone know?

HR use Cpanel with a custom theme (which its beautiful), Cpanel can be acquired at any of this dist. http://www.cpanel.net/dist.htm
AH use Alabanza's Control Panel (you can only get it if you have a server in their NOC if I'm not wrong).

Now to my next question....Custom themes? Is there a repository? Is there a way to create themes rather easily?

Check out the cpanel forums where theres a thread on all available cpanel skin sites.

I believe PixelBrick (http://www.pixelbrick.com) made it for them along with the layout.