When I made this, I didn't really have nostalgia or Those Days in mind, although I suppose it's inevitable how that'll factor into the votes of many.
For myself, no 90s nostalgia for these exists; I played the ones I played far later, incl. Doom last year, which I got really really into, and remain into.
I'm also not a big believer in art being dated in any real way; if it doesn't 'hold up' now, I suspect it wasn't terribly good to begin with, so when I say 'best', I suppose what I had in mind was: can you fire it up right now and have fun?
Dark Forces should have been on the list over Heretic.
ack, very good call! or maybe over Ken's Labyrinth, which was... not exactly a joke answer, maybe moreso a little recognition for Ken and his engine