Sorry for chiming in so late but I just wanted to give my two cents as well.
I always use the DOS version. First of all because I always keep my CM-32L (a MT-32 variant if you will) hooked to my PC and so I enjoy superior MIDI music.
Second, I use the DOS versions because they allow me to use VGA graphics instead of the hires SVGA ones the Windows (and DOS-Vesa-) versions use.
Because, really, Sierra only made part of the graphics hires at that point - like character portraits and inventory icons - the majority of the graphics (i.e. the backgrounds) are upscaled rather cheaply, which make them even more blocky and pixelized.
And then you can't even use a filter the smoothly upscale them.
So, my choice is always: Use the DOS (VGA) version and a nice scaler like 2xSAI (a lot of people prefer HQ2x but I feel that one distorts the picture too much).
Besides, I still think that these hires KQ6-character-portraits are, well, ugly.
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