I've also heard that the "Version Number" refers to the codebase/kernel version, but I don't believe it that much personally. They say XP was a major release, but it is not too much different then Win2k internally. The biggest thing is that it has a prettier front end.
If you look at it, MS had NT 4.0 for a while, then they released its successor - Windows 2000 Pro, which was labeled at 5.0 internally - indicating that it is technically NT 5. So it can only be logical to assume that Vista was also technically NT6, indicating a major update change - which it is, and that 7 being 6.1 is a relatively minor update - which it is. 7 is just basically a refresh, what vista should have been from the start.
That article brings up something else too, if 95/98/98SE/Me were all 4.x versions, wouldn't that mean Microsoft was essentially selling the exact same thing over and over?