I'm not averse to command line tools, in fact I used three and my own custom batch file to get this far
I was hoping there was something that would have allowed manual remapping from one pallete to another, but maybe if I can change the colours in the duke pallete to be more like doom's color range, and then load that pallette into each image, XWE will be able to do the rest. The only trouble is that Dooms blues are much more vibrant than Dukes, so XWE thinks the closest match is grey.
edit: Blech, pretty ugly result either way. You decide:
Or I could darken his uniform somewhat and turn him into a SWAT pig...
edit2: also tried cartoony style (third pic). I think that looks best, but I could probably optimise the colours a bit more.
That program is mint by the way

what a shame it "only" lets me edit pictures < 640x480