If you want a port of the PC version then I think the best ports are the Xbox versions which were included in the collector's edition of Doom³. This edition includes "
The Ultimate Doom" and "
Doom II" and two new levels, "Sewers" and "Betray". The standard edition of Doom³- Resurrection of Evil includes "
The Ultimate Doom" and "
Doom II", as well as Master Levels for Doom II. The Master levels was an expansion pack for Doom II and has 21 extra levels. The Xbox ports have all the PC levels for both games however, the 8 console-only levels which appeared on the Jaguar, Playstation, Saturn, and 3DO versions are omitted.
The Jaguar version has more levels than the SNES and 32X versions, and as many levels as the 3DO and GBA versions. It features 22 of the PC version's 27 levels, though many of them are simplified, plus 2 new levels (the levels titled "Tower of Babel" and "Hell Keep" are not the same as the PC levels of the same names). But hey have axed three enemies from the game: the Cyberdemon, the Spider Mastermind and the Spectre and I think the Cyberdemon is one of Doom's most iconic enemies.
The PlayStation and Saturn ports feature almost all the levels from the final releases of the PC version, though edited much like the Jaguar and 32X versions, with a few brand new levels designed by the Midway team, plus most of the levels from Doom II. But again they cut an enemy from the game, this time it's the Arch-Vile monster from Doom II, which is a very tough enemy on higher difficulties due to his fire attack and the fact that he resurrects enemies as long as he is alive. Worth noting is that the PS and Saturn ports don't have the Nightmare difficulty setting and they use passwords instead of save games for progression.
The SNES version of Doom features all five PC version levels that were missing from the Jaguar version, but is missing a different set of five levels instead, and like the 32X version, does not have any console-only levels. The levels included resemble the PC levels moreso than other ports. Also like the 32X version, the player's heads-up display doesn't utilize the whole screen, and enemies are only animated from the front, which means that they always face the player. That's quite a big deal because that means that the monsters won't fight each other and focus their attacks on you.
All in all it really comes down to personal preference when you weigh the pros and cons and pick what suits you the most. I am a massive Doom fan, if a console I own has a port of Doom or Wolfenstein then I buy it. Even if it is the exact same version I own for a different console. I just love the game to death
My personal choice for best port would be the Jaguar version. It plays really well with the controller, so don't be afraid of that, and when you have the overlay for the controller (or know which button is for which weapon) you can pick the weapon you want with just one button instead of repeatedly pressing a button to cycle through them like on the other versions.
What I CAN tell you with absolute certainty is that the 3DO version is the worst port. It runs in a small screen and at a low frame rate, though it includes the option to shrink the screen size even further, which allows the game to run faster.
To sum it all up:
Best port of the PC version: Doom on Xbox (via Doom³ collector's edition or Doom³ - Resurrection of evil)
Best version of the console ports: Atari Jaguar
