I noticed one day that the Skype icon in my Mac OS X menu bar was black.
Skype notes when I'm online, but what specifically does the black color indicate?
The icon becoming black and white is a change introduced in the latest revision (at least in 5.7).
It's basically just Skype becoming more dedicated to the OS X user interface, which doesn't encourage colorful menu bar items. Actually, people have often complained about the colored menu bar items before. I presume Skype finally addressed these concerns.
And in fact, Dropbox for example allows you to change the icon to black and white in its Preferences.
You can get the colors back by installing v5.6 from http://mac.oldapps.com/skype.php