Game engine recreations and source ports/FPS

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Earlier id games

ReflectionHLE: Conservative source port for Catacomb 3D series and Wolfenstein 3D, as well as Keen Dreams.
ECWolf: Source port for Wolfenstein 3D with support for widescreen and high resolution, and modding features.

Doom/id Tech 1 engine

id Tech 1 powered the original Doom, Doom 2 and Final Doom games, as well as Raven Software's Heretic and Hexen

UZDOOM: The successor to GZDoom, and the most popular Doom source port. Adds significant modding features and hardware rendering. Used by several commercial indie games.
Chocolate Doom: Conservative source port of Doom, strictly following the behavior and features of the original version, but for modern operating systems.
DSDA Doom: The successor to PrBoom+. Good accuracy to the original game through featurelevels, while at the same time supporting Boom and MBF21 extensions and (optional) hardware rendering. Popular with speedrunners.
Zandronum: The leading port for multiplayer Doom. Built on an older version of GZDoom.

The following ports are specific for Doom games on console

Doom 64 EX Plus: Updated fork of Kaiser's original Doom 64 EX. Adds new monsters and the ability to play the leaked alpha version of the game.
PsyDoom: A backport of Doom and Final Doom for the PS1.

Marathon engine

The engine used to power the Marathon trilogy of FPS games by Bungie, as well as games that licensed its engine.

Aleph One: Open source, freeware and cross-platform engine supporting Marathon, Marathon 2: Durandal and Marathon Infinity, as well as a host of mods made for these three games.

Build engine

Ken Silverman's Build Engine powered many FPS games in the mid and late 90s

EDuke32 and VoidSW: Duke Nukem 3D port with heavily extended CON scripting language. Used for the commercial game Ion Fury. The port VoidSW is for the game Shadow Warrior and is co-hosted with the EDuke32 repository. Has both the original software renderer as well as two hardware renderers (Polymost and Polymer) using OpenGL.
NBlood, Rednukem and PCExhumed: Sister projects to EDuke32 hosting reverse-engineered ports using the same backend. NBlood runs Blood and PCExhumed runs the DOS version of Powerslave. Rednukem is built on the original Atomic Edition source code for Duke Nukem 3D while also supporting Redneck Rampage, Redneck Rampage Rides Again and Duke Nukem 64. These ports are generally the most accurate to the original games.
NetDuke32: A multiplayer-focused port building on an older version of EDuke32. Only intended for multiplayer use
Raze: Port of multiple Build engine games running on the GZDoom backend. Hardware rendering only using its bespoke renderer, on OpenGL, GLES and Vulkan backends. Most games have bundled assets for widescreen resolution. Recommended for Mac users
BuildGDX: Port of multiple Build engine games, uses the GDX library for Java. Runs several games (Witchaven, TekWar, Legend of the Seven Paladins) not covered by the above ports. Has two hardware renderers (Polymost and its own PolyGDX) as well as software renderer. Most games have bundled assets for widescreen resolution.

These are not source ports in themselves, but software helpful for running games using the above ports

BuildLauncher

This is a frontend that helps launch addon content. Windows only for now.

NukemNet

Multiplayer launcher for several classic games including Duke Nukem 3D, Shadow Warrior and Blood.

Jedi Engine

Built in-house at LucasArts and adopting technologies previously developed for SCUMM games such as iMuse, the Jedi Engine went on only used in two games

The Force Engine: The successor to the XL Engine by the same developer. This is the only mature source port of the Jedi Engine and currently supports Dark Forces. Outlaws support is planned for future versions however.
DREAMM: Not a source port but worth mentioning. Emulates both Dark Forces and Outlaws along with many other games.

Quake series

The engines for Quake 1 and 2 are collectively considered as id Tech 2, and the engine for Quake 3 is known as id Tech 3. Both were licensed to other developers, and powered games such as Hexen 2, SiN, Soldier of Fortune 1&2, Daikatana, Kingpin, Jedi Outcast and Jedi Academy

DarkPlaces: Source port focusing on visually enhancing the original Quake. Used by Wrath: Aeon of Ruins.
Ironwail: High performance QuakeSpasm fork. Compatible with assets from 2021 remaster.
Q2 Pro: Multiplayer oriented port. Compatible with assets from 2023 remaster.

GoldSrc engine

Based on the Quake 1 engine, Valve's GoldSrc powered their breakthrough game Half-Life

Xash3d: Open source rewrite targeting compatibility with GoldSrc.