all games are not created equal

This is based solely on the PC versions of both titles.
As much as I try to be biased and say that Doom is the best PC title that I will always cherish til the day I die, I have to admit that Duke Nukem makes for a slightly better game.  It's essentially Doom on steroids (in same cases, literally).
The reason I let Duke slip out in front is cause of the farther exploration of levels.  With the ability to jump, crawl, swim and fly (with jetpack!), there's just more to explore. 
I will give Doom bonus points for monster and texture design though.  Everything in the game looks dark and gritty, almost gothic.  I can remember this being the first game my parents weren't really happy about me playing as a kid.
In terms of shock value though, my parents were even less pleased when I was playing Duke 3d.  You hit up a strip club in the second level!
Comparing weapons is tough because Doom basically laid out the standard types of weapons that would become staples in shooters.  Pistol, shotgun, automatic weapon (chaingun), rocket launcher, higher-damage multipurpose weapon (plasma), then the super rediculous destroy-all weapon (BFG).
I will give Duke 3D for trying hard to come up with a better and unique variety of weaponry.  The shrink ray is sure to raise some eyebrows, and the freeze cannon works well around corners.  Pipe bombs and lazer trip mines were also around before we even heard of Goldeneye for the 64. 
In the end, Doom will always bring back the most nostalgia for me, but Duke Nukem 3D just gave me that bit of variety I needed. 
Come get some!