There's just something about the original levels... it's incredible. I mean, take the movie theater in the first level for instance. There are three rows of blocky couch cushion chairs. There's a few enemies, a couple health kits. The walls are made out of curtains. If it were released today, it would be heavily criticized, and yet you rarely ever notice it while playing.
Anyway, I like the majority of the original levels, but if I had to narrow it down to 10 favourites, I'd pick (in no particular order):
E4L8 - Critical Mass
The most technologically stunning map in my opinion. Very effect-heavy. I especially like the room that goes dark for a moment and then spawns enemies in the room with you before turning the lights back on. And the building "collapses", can't forget that.
E3L8 - Hotel Hell
Awesome sector over sector effects. Very fun Dukematch level.
E4L2 - Duke Burger
There's nothing particularly fancy about this one, it's just a very solid level. I really like the secret ventilation passage into the kitchen (not the vent linked to the bathroom, the secret vent).
E4L11 - Area 51
It starts off a bit weak, but continues to get better and better. I remember being blown away by the hidden teleporter that went inside the Independence Day spaceship.
E2L4 - Fusion Station
I never really noticed how great Fusion Station was before, because I always jetpacked my way to the nuke button. The texturing and detail is fantastic.
E2L5 - Occupied Territory
This quickly became one of my two favourite Dukematch levels as a kid. Like most of the space episode, I can't explain why I like it so much.
E2L6 - Tiberius Station
Tiberius Station is another one of those maps that I just really enjoy for no particular reason.
E2L7 - Lunar Reactor
Tied with Occupied Territory for my favourite Dukematch level. This level has that area where you have to clear a chasm on the moon's surface, and then crawl back across the chasm through a breakable vent. I would personally bill that as being the most memorable area in the game.
E2L8 - Dark Side
The trains provided loads of entertainment in multiplayer. I prefer the N64 version of this map, but they're both good.
and uuhhmm
E4L9 - Derelict
This was probably the most unexpected and original level in the game. The sector over sector effects are great, but what I really like is the atmosphere of the bowels of the ship. The deeper it goes, the more lost and detached from the surface I feel.
Honourable Mention:
The brilliant sector tricks of E2L11 - Lunatic Fringe (very trippy).
The toppled building of E3L11 - Freeway (funny how the "freeway" is trapped by walls).
The variety of scenery in E3L5 - Movie Set (I especially like the Area 51 set).
The crashed mothership of E1L5 - The Abyss (another very memorable moment).
The destructible rocket in E1L6 - Launch Facility (pretty standard map otherwise).
and of course:
E1L1 - Hollywood Holocaust
E1L2 - Red Light District
E1L4 - Toxic Dump
I didn't forget about episode 1. It's great, I've just played it way too many times.
That was long. I'm hungry.