I only really got into Marathon several years ago and played Doom/Doom 2 not too long afterwards. IMHO there is a serious case to be made that Marathon is superior on every axis (music/sound excepted) but I absolutely understand why Doom had greater mass appeal. They're both a lot of fun but for me Marathon 2 is tops (and there are a LOT of homages to the series in later Bungie games - the 343 Guilty Spark escort level in Halo: CE is basically a redux of the alien ship crawl waiting-for-doors bullet hell level from Durandal).

I still have yet to finish Duke 3D. Next time I'm in between jobs I'll hit it up.