Mine has to be Derelict, the second last level of The Birth chapter. Huge unorthodox level where you start in the ocean.

I'll have to say a custom map called Alcatraz. As i recall it was a Multiplayer map for death matches... I recall having the highest kill count :P

Red Light District and not for the reasons you think. :P

I like identifiable usable worlds to play around in. It's sounds silly but phones, light switches, fire hydrants, TVs, toilets, pool tables etc are a blast for me. Nothing against the Dooms and Quakes out there but you spend those entire games in some generic alien world that have NOTHING but generic alien design and bland window dressing.

The submarine level was pretty cool and the one in town where he says "I ain't afraid of no Quake".
I'm also partial to the more contemporary 'realistic' levels.

You're thinking of Contra.

The Abyss Level, final level of first Episode. I liked general layout of level, though I hated it for the shrinking ray stuff.

Also there was some level with metro train in one of next Episodes, what level it was? I found this level to be quite confusing, which is exactly what I like.

Edit: according to wikia, it is probably Rabid Transit level in 3rd Episode. Not sure why I found it confusing though.

There was a metro level in Duke DC, was that it? That actually lead to a secret time travel level that was pretty sweet.

Now that I think about it, I guess most of the Duke it out in DC levels rank as my favorites though some of them were clearly rushed in design.

I'm going to avoid Duke 3D and say my favourite Duke level is Duke Burger from Duke Nukem Forever. Such silly fun.

Episode 3 of the original campaign does indeed feature an excellent level taking place in a subway, as well. It's called "Rabid Transit".

And man, I really hope Sunstorm's Duke 3D expansions come to GOG some day. I'd love to try them, especially after seeing the excellent work they did with Blood's "Cryptic Passage". I recently played the Duke Burger level in 3D's "Plutonium Pack", which is also a lot of fun, albeit pretty damn difficult.

Its the first level of the very first episode.

I agree, it is quite a kick in the balls.

My favorite was Area 51, the secret level from the 4th episode. I also like the Movie Set level from episode 3.

Does GOG have the Megaton edition by now?

I REMEMBER IT NOW!

Honestly the only thing I liked about that was the ability to chuck a pipe bomb into one of the cars with a baddie, step outside of the car, and and then set off the bomb watching Mr.Alien get blown to pieces. :P