SimCity 2000 was the first computer game I got that wasn't bundled with the PC I had, and I would play the game for hours every day for months. The version I played was the Windows 95 one. I still have the disc but now I have Windows 7 64 bit I can't install the game any more.
After playing the DOS version for a while I did notice a few differences.
One was the lack of a status bar. In the Windows 95 version there was a bar at the bottom of the screen that would tell you of problems in the city, things like "Water shortage reported". Some people might think that I'm confusing it with the newsreel from SimCity 3000 but it was different then that. Most of the time it was blank.
The game used the regular Windows interface, so you could have the game window run at the same size as your desktop resolution if you wanted.
Some of the animations were faster in the Windows 95 version, things like helicopters and trains.
An extra level of zoom. I think there was a help file that came with the Windows 95 version that told of some of the differences.
One thing I did notice with the DOS version is that some of the music tracks are longer.