Virtual Console

Virtual Console was an service made by Nintendo available during the online shopping eras of Wii (through Wii Shop Channel), Nintendo 3DS and Wii U (through Nintendo eShop).

Sega support
Sega supported all three variants of the Virtual Console, by either publishing games themselves or licensing games for Nintendo.

For Wii, Sega teamed up with M2 to deliver high-quality emulation of their legacy systems and Arcade boards in Nintendo's service. This was the start of one great alliance since the Sega Ages 2500 series on PlayStation 2, where several compilations in the series had emulation of SG-1000, Sega Master System, Sega Genesis, Sega Game Gear, and Sega Arcade games, varying by the titles themselves.

For Nintendo 3DS, Sega teamed up with M2 once again, this time, by bringing Sega Game Gear games into the service, alongside their own 3D Classics label of Arcade, Sega Genesis, Sega Master System, and SG-1000 games (the latter being available only on compilations).

For Wii U, Sega did choose to not bring games from their legacy systems and Arcade boards. Despite this, they allowed Nintendo to re-release their Game Boy Advance games on Wii U for Japan, as well as keeping most of the previous Wii Virtual Console games until the closure of the Wii Shop Channel in 2019. While not stated why, one can assume the low sales and polishing quality of Sega titles on Wii U (including Sonic Boom: Rise of Lyric) contributed to this decision.

Input support
Wii and Wii U iterations of Virtual Console had support for multiple controllers, depending of the system emulated. While Game Gear games on 3DS can be played only through their own internal button inputs, the Virtual Console menu can be summoned by touching the bottom screen.

Other systems such as TurboGrafx-16 can use a mix of different controllers (Wii Remote + GameCube controllers, Wii Remote + Wii U GamePad, etc.) or just a non-traditional Nintendo controller, such as MSX (generic USB keyboards can be used). Others can be played only with a single controller method, such as SNES and Nintendo 64 games on Wii (Classic Controller only) and Nintendo DS games on Wii U (Wii U GamePad only).

Sega Genesis / Mega Drive

 * Sega is the publisher of all games, with emulation handled by M2.
 * Suspend points are supported.
 * Most games can be played with the Wii Remote, Wii Remote + Classic Controller (either normal ou Pro), and/or GameCube Controller (the last, not being compatible with Wii U).
 * Several Sega Genesis games can only be played with the Classic Controller and/or GameCube Controller, namely the ones with 6 Button Arcade Pad support.
 * Several games supported online gameplay through Nintendo Wi-Fi Connection.
 * Sonic & Knuckles has Lock-On Technology support: It can virtually lock on with Sonic the Hedgehog (unlocking Blue Sphere), Sonic the Hedgehog 2 (unlocking Knuckles in Sonic the Hedgehog 2) and Sonic the Hedgehog 3 (unlocking Sonic the Hedgehog 3 & Knuckles), as long they are installed on the Wii's internal storage.
 * No Sega Genesis games were re-released in South Korea, despite the system being distributed by Samsung back in the 1990s.

Sega Master System

 * Sega is the publisher of all games, with emulation handled by M2.
 * Suspend points are supported.
 * All games can be played with the Wii Remote, Wii Remote + Classic Controller (either normal ou Pro), and/or GameCube Controller (the last, not being compatible with Wii U).
 * Several Sega Master System games supports FM Sound Unit emulation, being disabled by default.
 * No Sega Master System games were re-released in South Korea, despite the system being distributed by Samsung back in the 1980s and 1990s.

Arcade games

 * Games could range between 800 and 900 Nintendo Points.
 * For Sega Arcade games, Sega is the publisher of their respective games, with emulation handled by M2.
 * Most games can be played with the Wii Remote, Wii Remote + Classic Controller (either normal ou Pro) and/or GameCube Controller (the last, not being compatible with Wii U).
 * Several games supported online gameplay through Nintendo Wi-Fi Connection.
 * No Virtual Console Arcade games were re-released in South Korea.

Super Nintendo Entertainment System / Super Famicom

 * Nintendo is the publisher of all SNES games.
 * Games could range between 800 and 900 Nintendo Points.
 * All games must be played with Wii Remote + Classic Controller (either normal ou Pro) and/or GameCube Controller (the last, not being compatible with Wii U).
 * For Kirby's Avalanche / Kirby's Ghost Trap, Sega is mentioned in the instruction manual as one of the four copyright holders of the game. Despite this, the original version, Super Puyo Puyo, was not re-released in Japan.
 * The game was not re-released in South Korea, despite other NES, SNES, and N64 games being published in the region.

List of games and features (Nintendo 3DS)

 * For Game Gear games, Sega was the publisher of all games, with emulation handled by M2.
 * Several games support Gear-to-Gear Cable emulation through Local Play.
 * Restore points (save states) and suspension points are supported.
 * Multi-language menu depending on the language chosen in the system:
 * English, French, and Spanish for games re-released in the Americas.
 * If the HOME Menu is in Brazilian Portuguese, the in-game menu displays stuff in English instead.
 * Japanese for Japan-only games.
 * Multiple video modes are supported.
 * Button remapping, including rapid-fire support, is supported.
 * Special or original performance is supported.
 * No Game Gear games were re-released in South Korea and Southeast Asia.

List of games and features (Wii U)

 * Several games originally published by Sega for the Game Boy Advance were re-released on Wii U Virtual Console, but only in Japan. Nintendo is the publisher, with Game Boy Advance emulation handled by M2.
 * Games could be purchased for ¥715 Yen through Nintendo eShop in Japan.
 * All games include a digital version of the physical instruction manual that can only be viewed by the Wii U GamePad. All games can be played with the Wii U GamePad, Wii Remote, Wii Remote + Classic Controller (either normal ou Pro), and/or Wii U Pro Controller.
 * It is possible to switch video modes and select a video filter similar to HQ2X in the menu.
 * All games are playable in single-player modes only.
 * Features that required interactions with other devices, such as GameCube – Game Boy Advance link cable, are unsupported.

While not technically part of Virtual Console, Atlus' Trauma Team was re-released as part of Wii retail games available to download on Nintendo eShop and can be played on Wii Mode, otherwise known as vWii. It was sold in Japan and North America, being unreleased in Europe. While Atlus released the retail version in 2010 before Index Corporation sold Atlus to Sega Sammy Group, this re-release carries the "©ATLUS ©SEGA All rights reserved." copyright line on the Japanese Nintendo eShop page, which means Sega is the co-publisher of this re-release.

Wii Save Banner unused names
In certain region-exclusive games, Sega left out certain names from games that were not meant to be re-released (or ever released) in certain regions. Some Japanese-developed games that received International versions, remained exclusive to Japan, while some games that were developed by Western studios, remained exclusive to North America and Europe. They display some name oddities when transferring save data from one Wii region to another through SD cards, or using these foreign games through unauthorized methods by Nintendo.

These lists are just for informational purposes, they do not confirm if Sega was about to re-release these games worldwide.

Japanese to International

 * Bahamut Senki > Record of The Bahamu (the T from Bahamut was left out)
 * Chelnov > Atomic Runner
 * Dragon Slayer > Dragon Slayer VI
 * Dyna Brothers 2 Special > Dyna Brothers 2 Spec
 * Gynoug > Gynoug (Wings of Wor is not used)
 * Hokuto no Ken > Black Belt
 * Hokuto no Ken: Shin Seikimatsu Kyuuseishu Densetsu > Hokutonoken (Last Battle is not used)
 * Juusuu Kihei Leynos > Target Earth
 * Langrisser > Warsong
 * Langrisser II > Lungrisser2
 * Lord Monarch: Tokoton Sentou Densetsu > Lord Monarch
 * Pepenga Pengo > Pengo
 * Puyo Puyo (Arcade) > Puyo Pop (Puyo Puyo is not used, previously used for the Neo Geo Pocket Color version)
 * Puyo Puyo (Mega Drive) > Dr. Robotnik (Dr. Robotnik's Mean Bean Machine)
 * Puyo Puyo 2 (Arcade) > Puyo Pop 2
 * Puzzle & Action: Ichidant-R > IchidantoR (Japanese pronunciation is used)
 * Puzzle & Action: Tant-R > TantoR (Japanese pronunciation is used)

International to Japanese

 * Alex Kidd in Shinobi World > アレックスキッドの忍ワールド (Alex Kidd no Shinobi World)
 * Boogerman: A Pick and Flick Adventure > ブガーマン (Boogerman)
 * ClayFighter > クレイファイター (later officially used in Sega Genesis Mini 2)
 * Dr. Robotnik's Mean Bean Machine > ぷよぷよ (Puyo Puyo)
 * Mega Turrican > メガタリカン
 * Shanghai II: Dragon's Eye > 上海Ⅱ　ドラゴンズアイ
 * Sonic 3D Blast > ソニック３Ｄブラスト (previously using the European name of the Sega Saturn version, Sonic 3D Flickies' Island)
 * Sonic Chaos > ソニック＆テイルス (Sonic & Tails, used only for the Game Gear version)
 * ToeJam & Earl in Panic on Funkotron > トージャム＆アール２ (ToeJam & Earl 2, later re-releases uses a localized name of the English title)
 * Virtua Fighter 2 > バーチャファイター２ (name used before only for the Arcade and Sega Saturn versions)
 * Wonder Boy III: The Dragon's Trap > モンスターワールドⅡ　ドラゴンの罠 (Monster World II: Dragon no Wana, used only for the Game Gear version)

3DS / Wii U regional issues

 * By installing Puyo Puyo in a non-Japanese 3DS, the 3D banner displayed on the Top screen shows Dr. Robotnik's Mean Bean Machine in the Game Gear screen plus the 2D title banner. However, when starting the game, Puyo Puyo runs just as normal. This is the only Game Gear game with this oddity on Nintendo 3DS.
 * The reverse is true for Dr. Robotnik's Mean Bean Machine, but in a Japanese 3DS.
 * Due to limitations in the firmware, digital instruction manuals viewed through the HOME Menu cannot be displayed in out-of-region Wii U systems. This applies to Sega titles in Wii U Virtual Console: Trying to access them (through unauthorized methods by Nintendo) will display an error saying that it was not possible to read the digital instruction manual.