I really love these games, but before I buy them I would like to know if they (in particular moo2) is the "modified" windows version, or the original dos version?
(I'm a linux user and find things work much better in Dosbox than Wine)

I bought moo2 boxed from a store a few years ago (lost that copy now :S), and although the box said DOS, it was actually a version modified to work with windows.

Your boxed game probably had both the Win95.exe and DOS but gone is gone.

GOGs version installs the DOSBox version by default with the fan patch already included (highly recommended as I have seen no drawbacks to that patch). MoO2 that is. MoO1 has no Windows version.

Yep, MoO 1 is DOS only, while MoO 2 comes with DOS and Windows version.

Additionally, the Windows 95 version of MoO2 requires some messing around with to make work on a modern version of Windows. It's not just Linux users who have an easier time with the DOSBox version that is provided by default by GOG.

Well that's good to know!
I think I might have one last (probably fruitless) hunt for the original box in case it did, as you say, have the dos version though.