I've been a .net developer for over 12 years now and up until this point, have never given a second's thought to what the dot in dot net could mean besides being a dot. An initial google search on this topic hasn't cleared things up either:
https://encrypted.google.com/search?hl=en&gl=uk&q=.net+dot[
^]
I hate to kill the mystery off so quickly, but I think it's just a name, just as an Oracle database doesn't know everything despite it's name and the Eclipse IDE doesn't block out the sun or moon.