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[MrFlibble]

Just as the title suggests, this is an attempt to list free games that very closely follow a well-known product or franchise and can thus serve as an alternative to that particular game. These are mostly non-commercial projects, but some shareware games are also included.

What I have not included on the list are multiplayer-only games, browser-based games, and all kinds of free-to-play and "freemium" online products. I have also tried not to include projects that make use of original assets like graphics and sounds (unless authorized by original copyright holders, as is the case of T2002), so games like Mortal Kombat Project, Gods Deluxe or Return of the Triad are not on the list. Another thing out of the scope of this list are engine recreations that require original game assets to work.

Any further suggestions as to what games qualify as free alternatives are more than welcome

Update from 2022/02/10: A complete overhaul of the lists, using new groupings, which are hopefully more informative.

1. Original engine + free/libre game data
These are games based on the original code of their inspirations. Often, a free/libre game data set (levels, graphics, music) is created as a replacement for the original proprietary game data, while the playing mechanics remain the same, but sometimes, other aspects of gameplay undergo considerable alterations, which is reflected by the [mod] suffix in the list below.

In some cases, the source code/engine is still not public, but has been provided by owners to the community so that new free games or mods may be created.

Yet another case when the code is not available are various game construction sets that allow users to freely distribute games created with them. These are marked with the [toolkit] suffix.

Abuse

• fRaBs

Alien Shooter

• Theseus: Return of the Hero

The Bard's Tale

• The Bard's Lore [toolkit]
• The Bard's Quest [toolkit]

Crayon Physics

• Numpty Physics

Doom II

• Freedoom
• HacX [mod]
• Harmony [mod]

Duke Nukem 3D

• Mr The Killer [mod]

Freespace 2

• Wings of Dawn [mod]

Heretic

• Blasphemer

Hovertank 3D

• Robot Redemption

Lethal Tender

• Industrial Killers (ikillers.zip) [toolkit]

Quake

• LibreQuake
• Open Quartz
• Open Quartz 2
• Nexuiz Classic [mod]
• Rexuiz [mod]

Quake II

• CodeRED - Battle For Earth [mod]
• CodeRED - The Martian Chronicles [mod]
• Alien Arena [mod]
• D-Day Normandy [mod]
• Warsow [mod]

Quake III Arena

• OpenArena [mod]
• Acid Arena [mod]
• World of Pandman [mod]

Steel Panthers

• SPWW2 [mod]
• Steel Panthers: World at War [mod]

Steel Panthers II: Modern Battles

• SPMBT [mod]

Super-VGA Harrier

• Jaguar GR1: Strike Force Delta Zulu [toolkit]
• Tornado Squadron [toolkit]
• Skyhawk Attack [toolkit]

The Ultimate Doom

• Freedoom
• Chex Quest 3 [mod]
• REKKR [mod]

Wolfenstein 3-D

• Zillion 3D

2. Engine recreation + free/libre game data
Very similar to the above, but the original game source is not available in any form, so an attempt is made to recreate it from scratch and/or by means of reverse engineering. Usually such projects start by requiring the original game's data, and then a free/libre replacement data set is created by the community.

In some rare cases, the author of a recreation received permission from the copyright holders of the emulated game to use original proprietary game data, characters, title etc. These projects are marked with the [authr] suffix in the list.

Atomix

• Atomiks [authr]

The Bard's Tale Construction Set

• Bt Builder

Chip's Challenge

• Tile World

Command & Conquer: Red Alert

• Fractured Realms [mod]
• OpenHV [mod]

Commander Keen (second trilogy)

• Planet Cloudius IX

Digger (Windmill Software)

• Digger Remastered [authr]

Flight Sim Toolkit

• OpenFly

M.A.X.

• M.A.X. Reloaded

Panzer General

• LGeneral + K.u.k. General

Supaplex

• Open Supaplex [authr]

Total Annihilation

• Zero-K

Transport Tycoon Deluxe

• OpenTTD

UFO: Enemy Unknown

• UFO2000

Warcraft II

• Aleona's Tales (later releases merged with Wargus)
• Wyrmsun [mod]

3. Clones and remakes that faithfully recreate original mechanics
This is likely the most common type, with many projects being not only accurate reproductions of the original game mechanics, but often also trying to follow the original "look & feel" of their inspirations. At least some of these projects are motivated by the desire to create a FOSS alternative to a proprietary game for Linux users, or to fill in what is perceived as an empty niche for modern platforms.

Note that some of these games actually make rather drastic changes compared to the original titles they emulate, such as the transition to 3D graphics from 2D, or a cosmetic/thematic overhaul by using free software mascots as game characters for example.

A-Train

• FreeTrain

Age of Empires

• 0 A.D.
• The Fertile Crescent

Alien Breed

• Alien Assault II

Anno series

• Unknown Horizons

Arkanoid

• PopCorn

Battle Isle II

• Advanced Strategic Command
• Crimson Fields

BlockOut

• BockOut II [authr]

Blood

• Transfusion [authr]

Bomberman

• Mr.Boom
• Fracas

Boulder Dash

• GDash
• Rocks'n'Diamonds

Bust-a-Move/Puzzle Bobble

• Bobble Puzzle
• Frozen Bubble
• Zorx

Carrier Command

• Thunder&Lightning

Castlevania 2

• Castlevania 2: The Lecarde Chronicles [authr]

Civilisation V

• Unciv

Columns

• Bref

Command & Conquer

• Dark Konflict
• Future Conflict (fc_101pm.zip)

Crimsonland

• Bloodworks
• Violetland

D/Generation

• rE/Generation

Diablo

• FreedroidRPG
• FLARE
• Summoning Wars

Doom

• Anarch
• Shaw's Nightmare

Duke Nukem 1

• Dave Gnukem

Dungeon Keeper

• OpenDungeons

Elasto Mania

• XMoto

Elite

• Oolite

Empire Deluxe

• GEMpire

Escape Velocity

• NAEV

Forgotten Realms: Unlimited Adventures

• Dungeon Craft

The Great Giana Sisters

• Akiko and Minami
• Giana's Return
• Giana Worlds [authr]

Herzog Zwei

• Herzog 3D
• RAD - Rapid Aerial Deployment

Homeworld

• House Globe

King's Quest series

• King's Quest Remake [authr]
• King's Quest II Enhanced Edition [authr]
• King's Quest III [authr]

Knights and Merchants

• Knights Province

Lemmings

• Lix
• Pingus
• Hamsters

Lode Runner

• SDL Scavenger

The Lords of Midnight

• The Lords of Midnight PC [authr]

The Lost Vikings

• freeVikings

Magic Carpet

• Ogrian Carpet

Master of Monsters

• The Battle for Wesnoth

Master of Orion

• FreeOrion
• Remnants of the Precursors

Mechwarrior series

• Linwarrior 3D

Minecraft

• Manic Digger
• Minetest

Mortal Kombat

• Open Mortal

Nibbles

• Zmiy

OutRun

• RunOut

Oxyd

• Enigma

Pac-Man

• Open Greedy

Panzer General II

• Open General
• OpenPanzer / Panzer Marshal

Puzznic

• Wizznic!

Rise of the Triad

• Rise of the Wool Ball

RPG Maker

• EasyRPG
• Open RPG Maker

Secret Agent

• Special Agent

Sensible (World of) Soccer

• YSoccer

The Settlers II

• Widelands

The Settlers of Catan

• Pioneers

Sid Meier's Civilisation/Civilisation II

• Freeciv
• Great Nations
• Conquests
• C-evo
• Kingdoms

Sid Meier's Colonisation

• FreeCol

SimCity

• Lincity
• LinCity-NG
• OpenCity

SolarFox

• SolarWolf

Sonic the Hedgehog

• Open Surge

Star Wars: TIE Fighter

• Space Combat

StarCraft

• Priority: Survive

Stars!

• Stars! Nova

Stunts

• Ultimate Stunts

Super Hexagon

• Open Hexagon

Super Mario Bros.

• Secret Maryo Chronicles
• SuperTux

Super Monkey Ball

• Neverball

Tetris

• Super ACiD Block Attack

Thief: The Dark Project

• The Dark Mod

Total Annihilation

• Robotic War
• War Machines

Trailblazer

• Blazing Trails

Transport Tycoon

• Simutrans

Trugg

• Heartlight PC

Turrican II

• Hurrican
• T2002 [authr]

Ultima I

• The Kingdom of Syree

Ultima IV-V

• Haxima

Ultima VI

• IRE

Warcraft II

• Dark Oberon

Warlords II Deluxe

• LordsAWar!

Wing Commander

• Flight Commander

Wizardry VII

• Escape from the Maze
• Lost Hero

Worms

• Hedgewars
• WarMUX

X-COM/UFO

• X-Force: Fight for Destiny
• UFO: Alien Invasion