I actually had DN running on a 98 machine at one time by simply using the selective startup and not loading the autoexec.bat file to run it from dos as well as the Duke3D.
As for Wolf3D I ended up with the sequel RTWC running on the 64bit 7. I would need to make a 95 boot floppy to see 95 on VBox to accompany 98 there already!
The idea behind these sites however is to allow anyone to run an old Legacy version without any custom setups, VM wares on their own machine. For those that started off with 98, ME, 2K, or XP they never saw what 3.1 looked like being 95's predacessor there.