Sorry for the epic post; food for thought, maybe?
I have only played the PC version through once about 10 years ago, although I do own it and the Master Levels. Not being turned on by Revenant and Chaingunner spam, I'd have to say that (as usual) I preferred the PSX version.
For that version, here are my favourites, in order:
1. Vesperas: Beautiful to look at with the new sky texture, the Toxin Refinery music is enchanting and there are some nice views in this level. It looks and plays differently from anything in Doom/Doom 2 on the PSX.
2. Crater: Despite being mildly dumbed down with more basic architecture than the PC original and no Hell Barons, plus miles of empty corridors, this map evokes a strange, lonely atmosphere that works so well for the PSX port. There's a secret slime fall which my friends and I couldn't get our heads around - we thought it had to be a special area hiding bonuses. One downfall of Romero's style is that you don't get a good view, it has to be an area where you can go, so you can't stare at it and wonder what it would be like to get there.
3. Minos: A terrific exploration map, sinister and creepy with extremely unnerving music (think the wind roaring down pitch-black tunnels in the bowels of Hell). You can skip most of this map, which is weird, but it's very good to explore and the tension in the Hell Knight/Crusher room is unbearable since you can't save in-game. I'm actually working on a tribute map, working title Theseus, using the Plutonia textures.
4. Canyon: I just like this level. It's fun to explore, it's tough without being too hard and like most of the Final Doom maps, it's very different to the original levels, helping to kick FDoom off in its own direction.
5. Geryon: The disturbing and unsettling music is not the only distinctive thing about this map. I was still getting used to the beautiful night sky texture when this map loaded up. It should by rights be frustrating as gameplay is not entirely linear but it just plays really well with some nice views.
6. System Control: The only PSX map that gives you a berserk pack straight away and expects you to gib your way through a map. Nice. And the music track is one of the best of the PSX port.
To provide balance: I HATED all the Plutonia maps, they were too complex and very difficult for me back then (and probably still today). Heck was also pretty bad as it was too long, somewhat confusing compared to the more standard maps and just... no, not for me at all. Oh, and my friends and brother generally agreed with my assessment of the maps, so it would be interesting to hear from other PSX Doomers.