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[MrFlibble]

This is a spin-off of the extra content thread, but with a wider range of subjects to discuss, and definitely much more info to accommodate. The differences between various releases, and especially ports of a game can be quite huge, and may feature additions, cut-outs as well as other, sometimes rather unpredictable changes that may or may not affect gameplay. The differences can be split into the following categories:

Same platform re-releases

These are either updates that add new content or introduce major changes to a game, or releases on a more potent medium (e.g. a CD release compared to a floppy disk release) which allowed for more content to be included.

Corridor 7: Alien Invasion (DOS)
The CD version of the game has 10 more levels compared to the floppy disk version, an extra difficulty level setting, and a multiplayer option with 8 multiplayer maps.

Dune (DOS)
The CD version uses video footage from David Lynch's film for certain cutscenes, just like the Sega CD port. In the floppy version, cutscenes are rendered using the game's engine.

Flashback (DOS)
The CD version has new pre-rendered FMV sequences with music and sound.

Heretic: Shadow of the Serpent Riders (DOS)
The v1.3 upgrade brought two additional episodes to the game, essentially being a free add-on. The five-episode upgraded version is now standard, with the three-episode one having become obsolete.

Radix: Beyond the Void (DOS)
The v2.0 REMIX re-release of the game features major upgrades of graphics, tweaks and changes in many levels, some new weapon upgrades and a huge gameplay improvement in the form of a freely-controllable player's craft, as opposed to forced forward movement in all previous versions.

Tyrian (DOS)
Version 2.0 of the game added a new, fourth episode, a new game mode and more ships and weapons, and the Tyrian 2000 release (v3.0) included yet another episode in addition to the previous four, a few more ships and weapons, and some tweaks to balance the game.

UFO: Enemy Unknown (a.k.a. X-COM: UFO Defense) (DOS)
The CD version has some different sounds compared to the floppy version.

Special releases

Some games may have releases that are different from both public demos and full versions, either made for promotional or other reasons. These "special" semi-demo releases can sometimes only be obtained by specific means (for example, they may be shipped as a bonus with another product like a graphics card or a joystick, and are never sold separately) and cannot be distributed for free.

Descent: Destination Saturn
A 15-level (plus one secret level) demo (as opposed to the 7-level public shareware episode) of Descent shipped exclusively with certain hardware products (e.g. Gravis Phoenix). The levels 7 and 15 have been modified to move the boss battle from the former to the latter. There's a unique 5-level multiplayer mission set called "Modem Mayhem", instead of the standard "Total Chaos" set. This version of Descent supports add-ons (usually demo and shareware games do not support third-party add-ons and other modifications).

Descent 2: Destination Quartzon
A promotional version of Descent II shipped with certain hardware products (Wingman Extreme Joystick, Voodoo 3D video card) as a bonus. This version contains 8 levels from the full game (plus 2 secret levels), while the public demo only has the first three levels. In the intro screen, the game title is spelled as "Descent 2", as opposed to "Descent II" in the full game. Video cards with 3D accelerators were shipped with the Descent 2: Destination Quartzon 3D edition, which has no software renderer and can only be played with these 3D cards.

Half-Life: Day One
This is a demo version that contains the first one-fifth of the full game, and it was included as a bonus with certain video cards.

Rise of the Triad: The H.U.N.T. Begins Special Edition
To quote Joe Siegler (from the Rise of the Triad FAQ):

Originally Posted by Joe Siegler

"There is an extra version called Rise of the Triad: The HUNT Begins
SPECIAL EDITION. This is marketed in retail by LaserSoft. It is the
same as the regular shareware episode, except is has 3 extra levels, and
3 extra COMM-BAT Levels that are not available on ANY other version.
Apogee does not distribute this version, it is only available in stores
from LaserSoft."

At some point, this release has been discontinued, and the extra six levels were released for free by 3D Realms as an add-on to the full game.

Ports to other platforms

Porting a game to platforms different than its native one are quite common, and with the advent of new platforms, many rather old games may get a port too. During the transition from DOS to Windows on PCs, the porting of DOS games to Windows was widespread as well, with possible additions, fixes and enhancements not directly related to platform change.

In the past, console ports of arcade or PC games quite often had to introduce changes due to technological constraints such as cartridge memory or performance limitations. These changes result in partially cut content, or lower quality media like sounds and graphics. However, sometimes console ports feature profound differences in many aspects, and some of which can be considered as improvements over the original. Changes may also arise because of censoring, as some companies like Nintendo have a more family-friendly policy and ban explicit violence or sexual content from the games to be released for their platforms.

Command & Conquer (PlayStation)
The PlayStation port has five bonus (and one secret) missions, called the Special Ops, in addition to the original campaign and The Covert Operations add-on missions. This version features stereo music (something not found on PC), and certain music tracks are in their original form, with sound clips (thanks Nyerguds for all that info!).

Command & Conquer 64 (Nintendo 64)
The Nintendo 64 port is unique because of its true 3D graphics used both in-game and for video cutscenes, many of which are not duplicates or re-enactments of the original FMVs. There are also four extra bonus missions, two for each side, also called the Special Ops, which are different from the extra PlayStation version missions of the same name.

Command & Conquer Gold (Win9x)
Yeah, technically, C&C Gold is an official Windows port of the original DOS game. It added high resolution mode, a high-res interface, and Internet play capability.

Command & Conquer: Red Alert: Retaliation (PlayStation)
This is a "two-in-one" release of the Red Alert add-ons Counterstrike and Aftermath. Unlike the PC release, where the add-on missions can be played in any order, here the missions are arranged into campaigns (one for each side) and supplied with video briefings and cutscenes exclusive to this release. Some musical tracks are remixes of the originals ([i]Hell March, Crush, Radio 2 etc.), made by Frank Klepacki but not included in any of the PC versions of Red Alert (some of them made appearance on PC in another game of the series, Command & Conquer: Sole Survivor).

Doom
There's a very detailed in-depth FAQ describing the differences between the various ports of Doom, by Ledmeister. Read it here.

Doom 64 (Nintendo 64)
Essentially this is not a port of any other version of Doom but rather a sequel to Doom. It has basically the same game mechanics, but the levels, the storyline, and most graphics and sound effects are completely different. There is one new weapon and two enemy types not found in any other version of Doom, and the levels are also unique. More info about Doom 64 at Doom Wiki.

Duke Nukem 64 (Nintendo 64)
This version was heavily censored due to Nintendo's family-friendly policy, with swearing, alcohol, sexual and other dubious content removed. The game is not split into episodes, although the course of the levels is generally the same as in the retail PC version (with most levels fairly close to their PC counterparts as well, save for censorship changes), and some Atomic Edition levels are thrown in here and there too. The weapons, however, received a major overhaul, with some replaced and others acting differently (for example, Pistol and Shotgun can use two different ammo types in this version). Chaingun, RPG, Devastator and Freezethrower are all missing, and instead there are Sub-Machine Guns, Grenade Launcher, Missile Launcher and Plasma Cannon. The music and sky backgrounds are both missing from this version. There are a few multiplayer maps not found in other version of Duke Nukem 3D. The Cycloid Emperor is a full 3D polygon model. More info on this version at Duke Nukem Wiki.

Duke Nukem: Total Meltdown (PlayStation)
This port of Duke Nukem 3D features a whole new episode called "Plug 'n' Pray" in addition to the original three, several new enemy types and remixed music. Enemy sprites are redone in higher resolution for greater detail, and there are other graphical additions as well. More info on this version at Duke Nukem Wiki.

Dune (Sega CD)
This version uses video footage from David Lynch's film.

Flashback (3DO, CD-i)
These versions have pre-rendered FMV cinematic sequences, just like the PC CD version. Some fans prefer the original cinematics though.

Flashback (Sega CD)
In addition to the high-quality FMVs, this version has voiced-over in-game dialogues, and background music in every level.

Lemmings
Apparently, this game has quite a few differences between the ports, summed up in this Wikipedia article.

Powerslave (Play Station and Sega Saturn)
These two releases are very different from the PC version. First, they use a different engine called SlaveDriver, developed in-house by Lobotomy Software, as opposed to the licensed Build engine they used for the PC version. The SlaveDriver engine is supposedly more technologically advanced than the version of the Build engine used by Powerslave on PC. Secondly, while the levels are organized in linear progression in the PC version, the console versions have a hub system; the levels themselves are different and have different names (in the PC version, most levels have real Egyptian place names like Abu Simbel or Dendur; the console versions' levels have descriptive names like Sobek Mountain Shrine). All weapons in the console versions use a single ammo pool (even though some weapons fire bullets, while others various energy and/or magical projectiles). The Mummy Staff weapon is missing from the console versions; the Giant Spiders from the PC version are replaced by scorpion-like Terrainians.

Prince of Persia (Sega Genesis)
This port features improved graphics resembling those of the Macintosh version (but not identical) and slideshow intro and outro cutscenes, but otherwise it stays fairly close to the Amiga and PC versions. Some game mechanics like sword fighting or cutter trap function are not 100% identical though. The musical cues that accompany certain game events are sometimes mismatched.

Prince of Persia (Sega Mega Drive)
This version is very similar to the Genesis version, with the same graphics and sounds. However, this port also features background music in the levels, four more extra levels and new items like time-freezing or time-reversing potions. The introduction sequence is partially animated, but does not have any text.

Prince of Persia (Super Nintendo)
This port reproduces the game mechanics like sword fighting or trap functions more faithfully than the Sega ports, and has very nice improved graphics and background music. Additionally, there are eight new levels, making a total of 20, and the original levels have been revamped and expanded. The game had become much longer because of this, so the amount of time the player is given to complete the levels is doubled. New types of traps, enemies and mid-game bosses were added as well, further improving the game. In spite of all these profound changes, the game stays faithful to the atmosphere of the original. There's an intro sequence that uses the game engine.

Space Hulk (Amiga)
This version has different music compared to the PC version.

Starcraft 64 (Nintendo 64)
This release features both Starcraft and its add-on, Brood War, plus there is a secret bonus mission called Resurrection IV that is unique to this version. Also, the game tutorial is completely different from the PC version, and consists of two levels (the first focused on basic unit control and familiarizing the players with the interface, the other on base-building).

Starflight (Sega Mega Drive/Genesis)
The graphics and game mechanics are more advanced compared to other versions.

UFO: Enemy Unknown (a.k.a. X-COM: UFO Defense) (Amiga)
The Amiga version has somewhat lower quality graphics, but better sound.

UFO: Enemy Unknown (a.k.a. X-COM: UFO Defense) (PSX)
The PSX version has CD quality music (as opposed to MIDI music in the PC version) and several additional cutscenes.

Warcraft II: Battle.net Edition (Win9x)
The Windows port included both the original game and the add-on, new multiplayer maps, certain interface and control improvements (e.g. the food counter on the top bar alongside other resource meters, Starcraft-like), some fixes and, of course, Battle.net support. While the port was in development under the name Warcraft II Platinum, there were plans to include a new single-player Platinum campaign, but the idea was later rejected in favour of keeping the game as close to the original as possible.

Warcraft II: The Dark Saga (PlayStation)
This port includes both Tides of Darkness and Beyond the Dark Portal campaigns, has a new title screen, and introduces auto-build and auto-upgrade options.

Wing Commander I (3DO)
This port has voiceovers, different cutscenes and improved graphics.

Wing Commander III (3DO and PSX)
A few extra cutscenes were added compared to the PC version.

Wolfenstein 3D (Atari Jaguar and 3DO)
In these versions, enemy sprites have been redrawn in high resolution.

Wolfenstein 3D (Macintosh)
Enemy sprites have been redrawn in high resolution. German speech has been re-recorded by native German speakers.

Wolfenstein 3D (Super Nintendo)
This version was heavily censored, with blood and Nazi references completely removed. There are two new weapons: the flamethrower and the rocket launcher. Certain items and enemies from the Spear of Destiny prequel game are present in this version as well; however, some of the bosses from the PC version are missing, with Spear of Destiny bosses taking their place. Guard dogs have been replaced by mutant rats, presumably for censorship reasons. The levels have been vastly redesigned compared to the PC version, and are not split into separate episodes.