The Registry came about with Windows 3.1, which was released in 1992.
For a while, there were two fundamental difference "classes" of Windows OSs-one of which was a shell which ran on top of DOS. All of the 1.x, 2.x, and 3.x versions of Windows were this way, as were Windows 95, 98, and ME. Of course, 95 and later were designed do boot directly to the GUI, while with 3.1 and earlier one would generally boot to DOS first and then load Windows(although there were ways to make DOS automatically load Windows on booting).
In any case, the "other" version of Windows was Windows NT, which was designed from the start as a multi-user OS with a bunch of other features which everyone expects today. The first version of NT was released in 1993-it went through a few numerical versions, ending up at NT 4.0. Windows 2000 was effectively NT 5.0, and all Windows versions released after XP(inclusive) have been based on Windows NT.
The first version I used extensively was 2000, which got a lot of hate at the time but I actually had pretty good luck with it. We still have one computer kicking around the lab(the one running our UV-VIS Spectrophotometer) that is running Windows 2000, and it continues to function well. It was(and is) miles ahead of Windows ME, which was released around the same time and was a disaster.